rs10765509

Variant names:

• chr11-91999420-G-A
• rs10765509

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 0.656 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.632

Alfa AF: 0.604 Hom.: 36856

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10765509; hg19: chr11-91732586;