chr11-91924110-T-C

Variant names:

• chr11-91924110-T-C
• rs10501765

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.149 in 152,186 control chromosomes in the GnomAD database, including 1,967 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 (1967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 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: 22712 AN: 152068 Hom.: 1971 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.149 AC: 22709 AN: 152186 Hom.: 1967 Cov.: 32 AF XY: 0.149 AC XY: 11104 AN XY: 74404

African (AFR) AF: 0.0771 AC: 3204 AN: 41552

American (AMR) AF: 0.126 AC: 1926 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3464

East Asian (EAS) AF: 0.115 AC: 593 AN: 5176

South Asian (SAS) AF: 0.202 AC: 973 AN: 4816

European-Finnish (FIN) AF: 0.213 AC: 2255 AN: 10582

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12424 AN: 67980

Other (OTH) AF: 0.151 AC: 319 AN: 2114

Alfa AF: 0.174 Hom.: 3224

Bravo AF: 0.139

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	19
DANN	Benign	0.84
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs10501765; hg19: chr11-91657276;