rs10191411

Variant names:

• chr2-148630399-T-C
• rs10191411

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 0.558 in 152,108 control chromosomes in the GnomAD database, including 27,094 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 0.56 (27094 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.724 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: 0.559 AC: 84907 AN: 151990 Hom.: 27104 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.558 AC: 84893 AN: 152108 Hom.: 27094 Cov.: 33 AF XY: 0.552 AC XY: 41029 AN XY: 74372

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.557

Alfa AF: 0.674 Hom.: 52187

Bravo AF: 0.531

Asia WGS AF: 0.301 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10191411; hg19: chr2-149387968;