3-186862077-T-C

Variant names:

• chr3-186862077-T-C
• rs1403696

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 0.938 in 151,904 control chromosomes in the GnomAD database, including 67,382 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 0.94 (67382 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 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: 0.938 AC: 142359 AN: 151786 Hom.: 67369 Cov.: 30

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.938 AC: 142417 AN: 151904 Hom.: 67382 Cov.: 30 AF XY: 0.939 AC XY: 69765 AN XY: 74266

African (AFR) AF: 0.794 AC: 32793 AN: 41298

American (AMR) AF: 0.967 AC: 14745 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3461 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5179 AN: 5180

South Asian (SAS) AF: 0.988 AC: 4759 AN: 4816

European-Finnish (FIN) AF: 0.999 AC: 10560 AN: 10572

Middle Eastern (MID) AF: 0.983 AC: 285 AN: 290

European-Non Finnish (NFE) AF: 0.996 AC: 67712 AN: 68008

Other (OTH) AF: 0.955 AC: 2012 AN: 2106

Alfa AF: 0.927 Hom.: 38487

Bravo AF: 0.928

Asia WGS AF: 0.979 AC: 3402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.76
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs1403696; hg19: chr3-186579866;