rs10500965

Variant names:

• chr11-23575079-G-T
• rs10500965

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 0.152 in 151,886 control chromosomes in the GnomAD database, including 1,992 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 0.15 (1992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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: 0.151 AC: 22991 AN: 151768 Hom.: 1991 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.152 AC: 23017 AN: 151886 Hom.: 1992 Cov.: 32 AF XY: 0.156 AC XY: 11543 AN XY: 74212

African (AFR) AF: 0.150 AC: 6240 AN: 41472

American (AMR) AF: 0.166 AC: 2520 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3466

East Asian (EAS) AF: 0.411 AC: 2103 AN: 5122

South Asian (SAS) AF: 0.188 AC: 907 AN: 4824

European-Finnish (FIN) AF: 0.135 AC: 1424 AN: 10562

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8991 AN: 67910

Other (OTH) AF: 0.141 AC: 297 AN: 2108

Alfa AF: 0.144 Hom.: 211

Bravo AF: 0.153

Asia WGS AF: 0.268 AC: 931 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.71
DANN	Benign	0.66
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs10500965; hg19: chr11-23596625;