rs2734573

Variant names:

• chr6-31526961-C-A
• rs2734573

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.596

Alfa AF: 0.563 Hom.: 15238

Bravo AF: 0.610

Asia WGS AF: 0.490 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2734573; hg19: chr6-31494738;