3-138994862-A-G

Position:

• chr3-138994862-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.979

Gnomad4 AMR AF: 0.921

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.909

Alfa AF: 0.903 Hom.: 128166

Bravo AF: 0.930

Asia WGS AF: 0.923 AC: 3209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1511412; hg19: chr3-138713704;