chr3-101861806-A-G

Variant names:

• chr3-101861806-A-G
• rs601225

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 0.552 in 151,842 control chromosomes in the GnomAD database, including 24,272 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 0.55 (24272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 10 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 (AMR) allele frequency at 95% confidence interval = 0.656 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: 0.552 AC: 83753 AN: 151724 Hom.: 24256 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.552 AC: 83817 AN: 151842 Hom.: 24272 Cov.: 32 AF XY: 0.546 AC XY: 40548 AN XY: 74196

African (AFR) AF: 0.373 AC: 15422 AN: 41316

American (AMR) AF: 0.667 AC: 10191 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2090 AN: 3466

East Asian (EAS) AF: 0.461 AC: 2385 AN: 5168

South Asian (SAS) AF: 0.499 AC: 2401 AN: 4816

European-Finnish (FIN) AF: 0.541 AC: 5684 AN: 10512

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43742 AN: 67980

Other (OTH) AF: 0.571 AC: 1203 AN: 2106

Alfa AF: 0.614 Hom.: 16316

Bravo AF: 0.561

Asia WGS AF: 0.461 AC: 1603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.50
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs601225; hg19: chr3-101580650;