chr11-23575024-C-T

Variant names:

• chr11-23575024-C-T
• rs10500964

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 0.132 in 151,940 control chromosomes in the GnomAD database, including 1,608 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 0.13 (1608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 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: 0.132 AC: 19981 AN: 151822 Hom.: 1607 Cov.: 32

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.132 AC: 20004 AN: 151940 Hom.: 1608 Cov.: 32 AF XY: 0.135 AC XY: 10054 AN XY: 74274

African (AFR) AF: 0.0854 AC: 3540 AN: 41476

American (AMR) AF: 0.158 AC: 2399 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2049 AN: 5132

South Asian (SAS) AF: 0.168 AC: 812 AN: 4822

European-Finnish (FIN) AF: 0.135 AC: 1424 AN: 10580

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8976 AN: 67908

Other (OTH) AF: 0.127 AC: 269 AN: 2116

Alfa AF: 0.129 Hom.: 1431

Bravo AF: 0.131

Asia WGS AF: 0.246 AC: 858 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.72
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10500964; hg19: chr11-23596570;