rs2076188

Positions:

• chr6-11779266-T-C

Variant summary

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

The ENST00000506810.1(ADTRP):​c.-208+257A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,214 control chromosomes in the GnomAD database, including 32,972 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 0.63 (32941 hom., cov: 32)
  • Exomes 𝑓: 0.81 (31 hom.)
• Consequence: ADTRP ENST00000506810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11779266T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADTRP	ENST00000379415.6	c.-207-300A>G		intron_variant		5		ENSP00000368726.2
ADTRP	ENST00000506810.1	c.-208+257A>G		intron_variant		3		ENSP00000422927.1

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96435 AN: 152008 Hom.: 32931 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.635

GnomAD4 exome AF: 0.811 AC: 73 AN: 90 Hom.: 31 AF XY: 0.729 AC XY: 35 AN XY: 48

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.806

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.634 AC: 96470 AN: 152124 Hom.: 32941 Cov.: 32 AF XY: 0.628 AC XY: 46735 AN XY: 74400

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.637

Alfa AF: 0.734 Hom.: 62757

Bravo AF: 0.624

Asia WGS AF: 0.466 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.042
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2076188; hg19: chr6-11779499;