rs2734573

Variant names:

• chr6-31526961-C-A
• rs2734573

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 0.583 in 152,110 control chromosomes in the GnomAD database, including 26,387 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 0.58 (26387 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88636 AN: 151992 Hom.: 26355 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.583 AC: 88725 AN: 152110 Hom.: 26387 Cov.: 33 AF XY: 0.576 AC XY: 42870 AN XY: 74364

African (AFR) AF: 0.667 AC: 27683 AN: 41486

American (AMR) AF: 0.654 AC: 9990 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2261 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3187 AN: 5180

South Asian (SAS) AF: 0.476 AC: 2298 AN: 4830

European-Finnish (FIN) AF: 0.375 AC: 3965 AN: 10562

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37370 AN: 67994

Other (OTH) AF: 0.596 AC: 1255 AN: 2104

Alfa AF: 0.566 Hom.: 31213

Bravo AF: 0.610

Asia WGS AF: 0.490 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.39
DANN	Benign	0.39
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2734573; hg19: chr6-31494738;