3-101151010-T-C

Variant names:

• chr3-101151010-T-C
• rs6803634

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 0.69 in 152,096 control chromosomes in the GnomAD database, including 36,671 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 0.69 (36671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.690 AC: 104792 AN: 151978 Hom.: 36604 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.690 AC: 104920 AN: 152096 Hom.: 36671 Cov.: 32 AF XY: 0.693 AC XY: 51533 AN XY: 74330

African (AFR) AF: 0.798 AC: 33105 AN: 41500

American (AMR) AF: 0.719 AC: 10984 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3472

East Asian (EAS) AF: 0.851 AC: 4397 AN: 5168

South Asian (SAS) AF: 0.642 AC: 3098 AN: 4826

European-Finnish (FIN) AF: 0.656 AC: 6923 AN: 10560

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42227 AN: 67984

Other (OTH) AF: 0.673 AC: 1422 AN: 2114

Alfa AF: 0.667 Hom.: 5583

Bravo AF: 0.694

Asia WGS AF: 0.774 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.22
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6803634; hg19: chr3-100869854;