3-103662008-T-C

Variant names:

• chr3-103662008-T-C
• rs6775909

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 0.452 in 151,620 control chromosomes in the GnomAD database, including 16,807 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 0.45 (16807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68409 AN: 151500 Hom.: 16768 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.452 AC: 68511 AN: 151620 Hom.: 16807 Cov.: 32 AF XY: 0.460 AC XY: 34063 AN XY: 74048

African (AFR) AF: 0.630 AC: 26069 AN: 41364

American (AMR) AF: 0.482 AC: 7322 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1386 AN: 3470

East Asian (EAS) AF: 0.584 AC: 2966 AN: 5076

South Asian (SAS) AF: 0.589 AC: 2827 AN: 4802

European-Finnish (FIN) AF: 0.394 AC: 4160 AN: 10554

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22457 AN: 67852

Other (OTH) AF: 0.462 AC: 973 AN: 2108

Alfa AF: 0.387 Hom.: 35577

Bravo AF: 0.466

Asia WGS AF: 0.651 AC: 2264 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.67
DANN	Benign	0.59
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6775909; hg19: chr3-103380852;