3-166241576-G-A

Variant names:

• chr3-166241576-G-A
• rs1530207

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 0.716 in 151,522 control chromosomes in the GnomAD database, including 39,045 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 0.72 (39045 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108440 AN: 151404 Hom.: 39005 Cov.: 31

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.716 AC: 108540 AN: 151522 Hom.: 39045 Cov.: 31 AF XY: 0.723 AC XY: 53481 AN XY: 73994

African (AFR) AF: 0.766 AC: 31743 AN: 41418

American (AMR) AF: 0.673 AC: 10214 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2198 AN: 3468

East Asian (EAS) AF: 0.690 AC: 3534 AN: 5122

South Asian (SAS) AF: 0.782 AC: 3774 AN: 4824

European-Finnish (FIN) AF: 0.807 AC: 8517 AN: 10560

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.687 AC: 46481 AN: 67652

Other (OTH) AF: 0.683 AC: 1441 AN: 2110

Alfa AF: 0.705 Hom.: 11147

Bravo AF: 0.705

Asia WGS AF: 0.741 AC: 2570 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.064
DANN	Benign	0.17
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1530207; hg19: chr3-165959364;