rs11966356

Variant names:

• chr6-11783014-C-T
• rs11966356
• ENST00000379415.6:c.-207-4048G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADTRP	ENST00000379415.6	c.-207-4048G>A		intron_variant	Intron 2 of 5	5		ENSP00000368726.2

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

African (AFR) AF: 0.565 AC: 23311 AN: 41286

American (AMR) AF: 0.766 AC: 11676 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2777 AN: 3460

East Asian (EAS) AF: 0.547 AC: 2802 AN: 5124

South Asian (SAS) AF: 0.639 AC: 3072 AN: 4810

European-Finnish (FIN) AF: 0.868 AC: 9100 AN: 10478

Middle Eastern (MID) AF: 0.679 AC: 197 AN: 290

European-Non Finnish (NFE) AF: 0.832 AC: 56357 AN: 67758

Other (OTH) AF: 0.735 AC: 1550 AN: 2108

Alfa AF: 0.767 Hom.: 13008

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
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs11966356; hg19: chr6-11783247;