rs10911886

Positions:

• chr1-186568459-A-G

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 0.189 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.0453

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.192

Alfa AF: 0.166 Hom.: 448

Bravo AF: 0.205

Asia WGS AF: 0.137 AC: 478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10911886; hg19: chr1-186537591;