ENST00000379415.6:c.-207-5126G>A

Variant names:

• chr6-11784092-C-T
• rs1018383
• ENST00000379415.6:c.-207-5126G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000379415.6(ADTRP):​c.-207-5126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 151,806 control chromosomes in the GnomAD database, including 44,455 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 0.76 (44455 hom., cov: 29)
• Consequence: ADTRP ENST00000379415.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000379415.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADTRP	ENST00000379415.6	TSL:5	c.-207-5126G>A		intron	N/A	ENSP00000368726.2

Frequencies

GnomAD3 genomes AF: 0.758 AC: 114948 AN: 151690 Hom.: 44432 Cov.: 29

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.758 AC: 115011 AN: 151806 Hom.: 44455 Cov.: 29 AF XY: 0.754 AC XY: 55962 AN XY: 74190

African (AFR) AF: 0.628 AC: 25935 AN: 41312

American (AMR) AF: 0.746 AC: 11375 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2734 AN: 3466

East Asian (EAS) AF: 0.550 AC: 2842 AN: 5166

South Asian (SAS) AF: 0.642 AC: 3085 AN: 4808

European-Finnish (FIN) AF: 0.874 AC: 9204 AN: 10534

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.842 AC: 57213 AN: 67960

Other (OTH) AF: 0.750 AC: 1580 AN: 2108

Alfa AF: 0.799 Hom.: 6346

Bravo AF: 0.745

Asia WGS AF: 0.587 AC: 2039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.78
DANN	Benign	0.81
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1018383; hg19: chr6-11784325;