rs6808291

Variant names:

• chr3-114119743-T-A
• rs6808291

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 0.913 in 152,262 control chromosomes in the GnomAD database, including 64,082 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 (64082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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: 0.913 AC: 138880 AN: 152144 Hom.: 64067 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.913 AC: 138940 AN: 152262 Hom.: 64082 Cov.: 32 AF XY: 0.914 AC XY: 68074 AN XY: 74448

African (AFR) AF: 0.762 AC: 31614 AN: 41510

American (AMR) AF: 0.956 AC: 14634 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3419 AN: 3472

East Asian (EAS) AF: 0.978 AC: 5063 AN: 5176

South Asian (SAS) AF: 0.939 AC: 4539 AN: 4832

European-Finnish (FIN) AF: 0.979 AC: 10388 AN: 10612

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66142 AN: 68040

Other (OTH) AF: 0.933 AC: 1972 AN: 2114

Alfa AF: 0.937 Hom.: 8348

Bravo AF: 0.907

Asia WGS AF: 0.946 AC: 3289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.71
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs6808291; hg19: chr3-113838590;