rs11966356

chr6-11783014-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000379415.6(ADTRP):c.-207-4048G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 151,470 control chromosomes in the GnomAD database, including 42,383 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 0.74 (42383 hom., cov: 31)
• Consequence: ADTRP ENST00000379415.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769

Genes affected

ADTRP (HGNC:21214): (androgen dependent TFPI regulating protein) Enables hydrolase activity. Involved in several processes, including cell migration involved in sprouting angiogenesis; negative regulation of secretion by cell; and positive regulation of macromolecule metabolic process. Located in caveola and cell surface. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADTRP	ENST00000379415.6	c.-207-4048G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111612 AN: 151354 Hom.: 42368 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.676

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.737 AC: 111670 AN: 151470 Hom.: 42383 Cov.: 31 AF XY: 0.734 AC XY: 54294 AN XY: 73962

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.735

Alfa AF: 0.788 Hom.: 5966

Bravo AF: 0.727

Asia WGS AF: 0.584 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.68
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11966356; hg19: chr6-11783247;