3-138994862-A-G

Variant names:

• chr3-138994862-A-G
• rs1511412

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 0.928 in 152,272 control chromosomes in the GnomAD database, including 65,749 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 0.93 (65749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141220 AN: 152154 Hom.: 65699 Cov.: 32

Gnomad AFR AF: 0.979

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.928 AC: 141322 AN: 152272 Hom.: 65749 Cov.: 32 AF XY: 0.930 AC XY: 69204 AN XY: 74448

African (AFR) AF: 0.979 AC: 40697 AN: 41574

American (AMR) AF: 0.921 AC: 14080 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3151 AN: 3470

East Asian (EAS) AF: 0.971 AC: 5015 AN: 5166

South Asian (SAS) AF: 0.876 AC: 4230 AN: 4828

European-Finnish (FIN) AF: 0.937 AC: 9934 AN: 10602

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61243 AN: 68036

Other (OTH) AF: 0.909 AC: 1918 AN: 2110

Alfa AF: 0.907 Hom.: 266959

Bravo AF: 0.930

Asia WGS AF: 0.923 AC: 3209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.0
DANN	Benign	0.82
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1511412; hg19: chr3-138713704;