rs11766519

Positions:

• chr7-57524150-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.00835

Gnomad4 SAS AF: 0.0878

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.133

Alfa AF: 0.150 Hom.: 261

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11766519; hg19: chr7-57583856;