rs10500872

Positions:

• chr11-20224177-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;