rs10911901

Variant names:

• chr1-186654874-A-C
• rs10911901

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 0.264 in 151,782 control chromosomes in the GnomAD database, including 8,014 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 0.26 (8014 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 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: 0.264 AC: 39993 AN: 151664 Hom.: 7971 Cov.: 30

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0482

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.264 AC: 40094 AN: 151782 Hom.: 8014 Cov.: 30 AF XY: 0.257 AC XY: 19050 AN XY: 74210

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0480

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.0813

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.257

Alfa AF: 0.185 Hom.: 1850

Bravo AF: 0.286

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.74
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10911901; hg19: chr1-186624006; COSMIC: COSV70100224;