rs10765509

Variant names:

• chr11-91999420-G-A
• rs10765509

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 0.656 in 151,836 control chromosomes in the GnomAD database, including 34,654 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 0.66 (34654 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.953
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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: 0.656 AC: 99507 AN: 151718 Hom.: 34599 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.656 AC: 99611 AN: 151836 Hom.: 34654 Cov.: 31 AF XY: 0.645 AC XY: 47802 AN XY: 74162

African (AFR) AF: 0.899 AC: 37278 AN: 41452

American (AMR) AF: 0.572 AC: 8709 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2150 AN: 3468

East Asian (EAS) AF: 0.310 AC: 1592 AN: 5134

South Asian (SAS) AF: 0.475 AC: 2282 AN: 4802

European-Finnish (FIN) AF: 0.527 AC: 5545 AN: 10522

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40131 AN: 67922

Other (OTH) AF: 0.632 AC: 1332 AN: 2106

Alfa AF: 0.613 Hom.: 47904

Bravo AF: 0.672

Asia WGS AF: 0.388 AC: 1348 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.0
DANN	Benign	0.46
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs10765509; hg19: chr11-91732586;