rs10501467

Variant names:

• chr11-80524745-T-C
• rs10501467

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 0.17 in 152,134 control chromosomes in the GnomAD database, including 2,501 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 0.17 (2501 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.294 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: 0.170 AC: 25812 AN: 152016 Hom.: 2498 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.170 AC: 25815 AN: 152134 Hom.: 2501 Cov.: 32 AF XY: 0.168 AC XY: 12504 AN XY: 74376

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.0355

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.184

Alfa AF: 0.202 Hom.: 3088

Bravo AF: 0.159

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	12
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501467; hg19: chr11-80235789;