rs4750277

Variant names:

• chr10-12872521-C-A
• rs4750277

Your query was ambiguous. Multiple possible variants found:

• chr10-12872521-C-A
• chr10-12872521-C-G
• chr10-12872521-C-T

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 0.774 in 152,030 control chromosomes in the GnomAD database, including 45,997 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 0.77 (45997 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 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: 0.774 AC: 117592 AN: 151912 Hom.: 45973 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.774 AC: 117667 AN: 152030 Hom.: 45997 Cov.: 31 AF XY: 0.773 AC XY: 57433 AN XY: 74324

African (AFR) AF: 0.672 AC: 27807 AN: 41400

American (AMR) AF: 0.736 AC: 11248 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2928 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3259 AN: 5166

South Asian (SAS) AF: 0.770 AC: 3717 AN: 4828

European-Finnish (FIN) AF: 0.847 AC: 8969 AN: 10588

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.839 AC: 57057 AN: 67978

Other (OTH) AF: 0.778 AC: 1644 AN: 2112

Alfa AF: 0.816 Hom.: 230399

Bravo AF: 0.758

Asia WGS AF: 0.739 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs4750277; hg19: chr10-12914521;