rs10911877

Variant names:

• chr1-186537480-G-A
• rs10911877

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 0.345 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.510 AC: 21084 AN: 41354

American (AMR) AF: 0.389 AC: 5942 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1097 AN: 3466

East Asian (EAS) AF: 0.423 AC: 2171 AN: 5134

South Asian (SAS) AF: 0.263 AC: 1265 AN: 4814

European-Finnish (FIN) AF: 0.219 AC: 2314 AN: 10544

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.256 AC: 17378 AN: 67954

Other (OTH) AF: 0.359 AC: 757 AN: 2106

Alfa AF: 0.319 Hom.: 1831

Bravo AF: 0.370

Asia WGS AF: 0.399 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.35
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10911877; hg19: chr1-186506612;