chr11-102516960-C-T

Variant names:

• chr11-102516960-C-T
• rs17098236

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0805 in 152,238 control chromosomes in the GnomAD database, including 494 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 0.081 (494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0997 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: 0.0804 AC: 12224 AN: 152120 Hom.: 490 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.0144

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0805 AC: 12259 AN: 152238 Hom.: 494 Cov.: 32 AF XY: 0.0778 AC XY: 5792 AN XY: 74432

African (AFR) AF: 0.102 AC: 4247 AN: 41528

American (AMR) AF: 0.0745 AC: 1139 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0727 AC: 252 AN: 3464

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5184

South Asian (SAS) AF: 0.0431 AC: 208 AN: 4826

European-Finnish (FIN) AF: 0.0509 AC: 540 AN: 10602

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0824 AC: 5607 AN: 68018

Other (OTH) AF: 0.0762 AC: 161 AN: 2114

Alfa AF: 0.0816 Hom.: 813

Bravo AF: 0.0830

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.65
DANN	Benign	0.49
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17098236; hg19: chr11-102387691;