rs2495774

chr10-123172570-C-Achr10-123172570-C-Gchr10-123172570-C-T

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 0.625 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.636

Alfa AF: 0.517 Hom.: 28526

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2495774; hg19: chr10-124932086;