rs2894347

Variant names:

• chr10-76869349-G-A
• rs2894347

Your query was ambiguous. Multiple possible variants found:

• chr10-76869349-G-A
• chr10-76869349-G-C

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 0.594 in 152,000 control chromosomes in the GnomAD database, including 27,544 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 0.59 (27544 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 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: 0.594 AC: 90249 AN: 151882 Hom.: 27505 Cov.: 31

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.594 AC: 90336 AN: 152000 Hom.: 27544 Cov.: 31 AF XY: 0.596 AC XY: 44303 AN XY: 74276

African (AFR) AF: 0.744 AC: 30847 AN: 41468

American (AMR) AF: 0.561 AC: 8560 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1621 AN: 3466

East Asian (EAS) AF: 0.488 AC: 2507 AN: 5140

South Asian (SAS) AF: 0.545 AC: 2626 AN: 4820

European-Finnish (FIN) AF: 0.571 AC: 6019 AN: 10546

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36404 AN: 67976

Other (OTH) AF: 0.538 AC: 1132 AN: 2106

Alfa AF: 0.545 Hom.: 92899

Bravo AF: 0.595

Asia WGS AF: 0.514 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.26
DANN	Benign	0.48
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2894347; hg19: chr10-78629107;