rs10195263

chr2-150869278-G-Achr2-150869278-G-C

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 0.973 in 152,282 control chromosomes in the GnomAD database, including 72,101 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 0.97 (72101 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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 (AMR) allele frequency at 95% confidence interval = 0.971 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: 0.973 AC: 148047 AN: 152164 Hom.: 72045 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.973 AC: 148162 AN: 152282 Hom.: 72101 Cov.: 31 AF XY: 0.973 AC XY: 72447 AN XY: 74450

Gnomad4 AFR AF: 0.970

Gnomad4 AMR AF: 0.981

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.957

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.977

Gnomad4 OTH AF: 0.973

Alfa AF: 0.976 Hom.: 122792

Bravo AF: 0.972

Asia WGS AF: 0.919 AC: 3198 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	0.70
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10195263; hg19: chr2-151725792;