rs2495774

Variant names:

• chr10-123172570-C-A
• rs2495774

Your query was ambiguous. Multiple possible variants found:

• chr10-123172570-C-A
• chr10-123172570-C-G
• chr10-123172570-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 0.625 in 152,156 control chromosomes in the GnomAD database, including 32,252 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 (32252 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 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: 0.625 AC: 95017 AN: 152038 Hom.: 32205 Cov.: 33

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.625 AC: 95119 AN: 152156 Hom.: 32252 Cov.: 33 AF XY: 0.626 AC XY: 46574 AN XY: 74360

African (AFR) AF: 0.889 AC: 36938 AN: 41550

American (AMR) AF: 0.637 AC: 9746 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3472

East Asian (EAS) AF: 0.801 AC: 4138 AN: 5164

South Asian (SAS) AF: 0.646 AC: 3116 AN: 4824

European-Finnish (FIN) AF: 0.445 AC: 4708 AN: 10576

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32660 AN: 67962

Other (OTH) AF: 0.636 AC: 1342 AN: 2110

Alfa AF: 0.541 Hom.: 75573

Bravo AF: 0.654

Asia WGS AF: 0.671 AC: 2327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0010
DANN	Benign	0.61
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2495774; hg19: chr10-124932086;