rs3094572

Variant names:

• chr6-29513216-T-C
• rs3094572

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 0.635 in 152,110 control chromosomes in the GnomAD database, including 30,929 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 0.63 (30929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.762 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: 0.635 AC: 96447 AN: 151992 Hom.: 30883 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.635 AC: 96550 AN: 152110 Hom.: 30929 Cov.: 32 AF XY: 0.638 AC XY: 47436 AN XY: 74350

African (AFR) AF: 0.689 AC: 28555 AN: 41468

American (AMR) AF: 0.568 AC: 8694 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1705 AN: 3472

East Asian (EAS) AF: 0.676 AC: 3485 AN: 5158

South Asian (SAS) AF: 0.783 AC: 3773 AN: 4818

European-Finnish (FIN) AF: 0.672 AC: 7111 AN: 10584

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41265 AN: 67996

Other (OTH) AF: 0.609 AC: 1285 AN: 2110

Alfa AF: 0.616 Hom.: 85506

Bravo AF: 0.629

Asia WGS AF: 0.769 AC: 2675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.29
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs3094572; hg19: chr6-29480993;