chr11-91102948-T-A

Variant names:

• chr11-91102948-T-A
• rs10501751

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 0.149 in 152,134 control chromosomes in the GnomAD database, including 1,813 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 0.15 (1813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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: 0.149 AC: 22701 AN: 152016 Hom.: 1811 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.149 AC: 22704 AN: 152134 Hom.: 1813 Cov.: 32 AF XY: 0.149 AC XY: 11083 AN XY: 74366

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.151

Alfa AF: 0.135 Hom.: 174

Bravo AF: 0.155

Asia WGS AF: 0.129 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501751; hg19: chr11-90836116;