rs10189050

Variant names:

• chr2-22901686-C-A
• rs10189050

Your query was ambiguous. Multiple possible variants found:

• chr2-22901686-C-A
• chr2-22901686-C-G
• chr2-22901686-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 0.924 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.979 AC: 40691 AN: 41560

American (AMR) AF: 0.931 AC: 14234 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2926 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5174 AN: 5176

South Asian (SAS) AF: 0.955 AC: 4572 AN: 4786

European-Finnish (FIN) AF: 0.949 AC: 10071 AN: 10608

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60058 AN: 68022

Other (OTH) AF: 0.920 AC: 1944 AN: 2114

Alfa AF: 0.898 Hom.: 114643

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
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10189050; hg19: chr2-23124558;