rs11766519

Variant names:

• chr7-57524150-T-C
• rs11766519

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 0.125 in 152,152 control chromosomes in the GnomAD database, including 1,652 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 0.13 (1652 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.907
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 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: 0.125 AC: 19068 AN: 152034 Hom.: 1655 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.00833

Gnomad SAS AF: 0.0887

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.125 AC: 19055 AN: 152152 Hom.: 1652 Cov.: 32 AF XY: 0.122 AC XY: 9096 AN XY: 74378

African (AFR) AF: 0.0324 AC: 1345 AN: 41574

American (AMR) AF: 0.129 AC: 1967 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3472

East Asian (EAS) AF: 0.00835 AC: 43 AN: 5152

South Asian (SAS) AF: 0.0878 AC: 424 AN: 4830

European-Finnish (FIN) AF: 0.125 AC: 1322 AN: 10600

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12761 AN: 67972

Other (OTH) AF: 0.133 AC: 281 AN: 2106

Alfa AF: 0.123 Hom.: 631

Bravo AF: 0.123

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	18
DANN	Benign	0.71
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs11766519; hg19: chr7-57583856;