rs10500956

Variant names:

• chr11-23456909-C-T
• rs10500956

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 0.163 in 152,002 control chromosomes in the GnomAD database, including 2,185 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 0.16 (2185 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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: 0.163 AC: 24713 AN: 151884 Hom.: 2184 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.163 AC: 24721 AN: 152002 Hom.: 2185 Cov.: 32 AF XY: 0.167 AC XY: 12440 AN XY: 74298

African (AFR) AF: 0.122 AC: 5066 AN: 41466

American (AMR) AF: 0.153 AC: 2341 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 277 AN: 3470

East Asian (EAS) AF: 0.132 AC: 678 AN: 5150

South Asian (SAS) AF: 0.241 AC: 1160 AN: 4816

European-Finnish (FIN) AF: 0.254 AC: 2676 AN: 10538

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12049 AN: 67982

Other (OTH) AF: 0.123 AC: 259 AN: 2112

Alfa AF: 0.168 Hom.: 6501

Bravo AF: 0.150

Asia WGS AF: 0.216 AC: 753 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.3
DANN	Benign	0.72
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs10500956; hg19: chr11-23478455;