rs10500872

Variant names:

• chr11-20224177-T-C
• rs10500872

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 0.142 in 152,156 control chromosomes in the GnomAD database, including 1,625 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 0.14 (1625 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 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: 0.142 AC: 21652 AN: 152038 Hom.: 1622 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0981

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.142 AC: 21654 AN: 152156 Hom.: 1625 Cov.: 32 AF XY: 0.139 AC XY: 10376 AN XY: 74404

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.0981

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.161

Alfa AF: 0.158 Hom.: 2807

Bravo AF: 0.145

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500872; hg19: chr11-20245723;