rs10911886

Variant names:

• chr1-186568459-A-G
• rs10911886

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 0.189 in 152,038 control chromosomes in the GnomAD database, including 3,699 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 0.19 (3699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 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: 0.189 AC: 28678 AN: 151920 Hom.: 3676 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0456

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.189 AC: 28747 AN: 152038 Hom.: 3699 Cov.: 32 AF XY: 0.184 AC XY: 13660 AN XY: 74320

African (AFR) AF: 0.362 AC: 14991 AN: 41430

American (AMR) AF: 0.158 AC: 2415 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3468

East Asian (EAS) AF: 0.0453 AC: 235 AN: 5186

South Asian (SAS) AF: 0.122 AC: 586 AN: 4818

European-Finnish (FIN) AF: 0.0672 AC: 711 AN: 10586

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8591 AN: 67968

Other (OTH) AF: 0.192 AC: 405 AN: 2108

Alfa AF: 0.171 Hom.: 488

Bravo AF: 0.205

Asia WGS AF: 0.137 AC: 478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.80
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs10911886; hg19: chr1-186537591;