3-61532442-A-G

Variant names:

• chr3-61532442-A-G
• rs1320173

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 0.471 in 151,968 control chromosomes in the GnomAD database, including 16,947 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 0.47 (16947 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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: 0.471 AC: 71580 AN: 151848 Hom.: 16943 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.471 AC: 71617 AN: 151968 Hom.: 16947 Cov.: 32 AF XY: 0.471 AC XY: 34977 AN XY: 74260

African (AFR) AF: 0.442 AC: 18314 AN: 41472

American (AMR) AF: 0.465 AC: 7109 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1465 AN: 3468

East Asian (EAS) AF: 0.644 AC: 3305 AN: 5130

South Asian (SAS) AF: 0.496 AC: 2387 AN: 4810

European-Finnish (FIN) AF: 0.456 AC: 4806 AN: 10542

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32701 AN: 67946

Other (OTH) AF: 0.473 AC: 998 AN: 2110

Alfa AF: 0.478 Hom.: 21676

Bravo AF: 0.469

Asia WGS AF: 0.555 AC: 1932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.31
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs1320173; hg19: chr3-61518116;