rs10189050

chr2-22901686-C-Achr2-22901686-C-Gchr2-22901686-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 0.924 in 152,230 control chromosomes in the GnomAD database, including 65,219 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 0.92 (65219 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.924 AC: 140588 AN: 152112 Hom.: 65159 Cov.: 31

Gnomad AFR AF: 0.979

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.924 AC: 140707 AN: 152230 Hom.: 65219 Cov.: 31 AF XY: 0.928 AC XY: 69077 AN XY: 74416

Gnomad4 AFR AF: 0.979

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.949

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.920

Alfa AF: 0.888 Hom.: 76256

Bravo AF: 0.925

Asia WGS AF: 0.974 AC: 3387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	11
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10189050; hg19: chr2-23124558;