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LYFE SCIENCES
Project: HERA
NM_032607.3:c.313G>A
p.Gly105Arg  ·  CREB3L3
ACMG/AMP
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Classification rationale
1

The CREB3L3 c.313G>A (p.Gly105Arg, p.G105R) variant has been reported in ClinVar as Benign with criteria provided by a single submitter representing 2 clinical laboratory submissions.

clinvar ↗
2

This variant is common in population databases, with gnomAD v2.1 showing a total allele frequency of 0.37177% and an East Asian allele frequency of 3.44274%, and gnomAD v4.1 showing a total allele frequency of 0.21551% and an East Asian allele frequency of 3.43413%, which is above the default benign population thresholds.

gnomad_v2 ↗ gnomad_v4 ↗
3

Computational evidence does not support a damaging effect, with SpliceAI predicting no significant splice impact (maximum delta score 0.02), REVEL 0.257, and BayesDel -0.423809.

spliceai ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
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Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This variant is present in gnomAD v2.1 (AF= 0.0037177; MAF= 0.37177%, 1047/281626 alleles, homozygotes = 14) and has highest observed frequency in the East Asian population (AF= 0.0344274; MAF= 3.44274%, 686/19926 alleles, homozygotes = 13); grpmax FAF= 0.0321736.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 0.00215512; MAF= 0.21551%, 3478/1613834 alleles, homozygotes = 37) and has highest observed frequency in the East Asian population (AF= 0.0343413; MAF= 3.43413%, 1540/44844 alleles, homozygotes = 31); grpmax FAF= 0.0329142.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Benign (2 clinical laboratories).
ClinVar ↗
03
Functional
No functional summary recorded.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.257. BayesDel score = -0.423809.
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
06
Cancer hotspots Not found
No cancer hotspot summary recorded.
Hotspots ↗