rs10911877

Variant names:

• chr1-186537480-G-A
• rs10911877

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 0.345 in 151,834 control chromosomes in the GnomAD database, including 10,007 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 0.34 (10007 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 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: 0.344 AC: 52212 AN: 151716 Hom.: 9962 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.345 AC: 52307 AN: 151834 Hom.: 10007 Cov.: 32 AF XY: 0.344 AC XY: 25524 AN XY: 74224

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.359

Alfa AF: 0.315 Hom.: 1742

Bravo AF: 0.370

Asia WGS AF: 0.399 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10911877; hg19: chr1-186506612;