4-137866906-A-G

Variant names:

• chr4-137866906-A-G
• rs2313982

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.912 in 152,160 control chromosomes in the GnomAD database, including 63,284 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.91 (63284 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138583 AN: 152042 Hom.: 63230 Cov.: 31

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.932

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.912 AC: 138696 AN: 152160 Hom.: 63284 Cov.: 31 AF XY: 0.910 AC XY: 67711 AN XY: 74378

African (AFR) AF: 0.877 AC: 36378 AN: 41498

American (AMR) AF: 0.949 AC: 14507 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3246 AN: 3472

East Asian (EAS) AF: 0.944 AC: 4873 AN: 5164

South Asian (SAS) AF: 0.972 AC: 4690 AN: 4824

European-Finnish (FIN) AF: 0.865 AC: 9152 AN: 10576

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62704 AN: 68022

Other (OTH) AF: 0.931 AC: 1971 AN: 2116

Alfa AF: 0.923 Hom.: 111563

Bravo AF: 0.916

Asia WGS AF: 0.928 AC: 3226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.73
PhyloP100		-0.0070

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2313982; hg19: chr4-138788060;