11-102519457-C-T

Variant names:

• chr11-102519457-C-T
• rs495041

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 0.3 in 151,920 control chromosomes in the GnomAD database, including 8,989 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 0.30 (8989 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 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: 0.300 AC: 45474 AN: 151802 Hom.: 8960 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.300 AC: 45553 AN: 151920 Hom.: 8989 Cov.: 32 AF XY: 0.304 AC XY: 22574 AN XY: 74248

African (AFR) AF: 0.537 AC: 22251 AN: 41426

American (AMR) AF: 0.297 AC: 4532 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3468

East Asian (EAS) AF: 0.532 AC: 2744 AN: 5162

South Asian (SAS) AF: 0.355 AC: 1706 AN: 4808

European-Finnish (FIN) AF: 0.152 AC: 1603 AN: 10534

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11166 AN: 67944

Other (OTH) AF: 0.277 AC: 584 AN: 2110

Alfa AF: 0.205 Hom.: 6122

Bravo AF: 0.319

Asia WGS AF: 0.453 AC: 1575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.46
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs495041; hg19: chr11-102390188;