rs10495712

chr2-20973240-A-Gchr2-20973240-A-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 0.774 in 152,180 control chromosomes in the GnomAD database, including 45,792 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 (45792 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 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: 0.774 AC: 117647 AN: 152062 Hom.: 45767 Cov.: 33

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.774 AC: 117722 AN: 152180 Hom.: 45792 Cov.: 33 AF XY: 0.774 AC XY: 57571 AN XY: 74398

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.813

Alfa AF: 0.752 Hom.: 57366

Bravo AF: 0.776

Asia WGS AF: 0.870 AC: 3026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.63
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495712; hg19: chr2-21196112;