6-11714573-G-A

Variant names:

• chr6-11714573-G-A
• rs3734273
• NM_032744.4:c.659-61C>T

Variant summary

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

The NM_032744.4(ADTRP):​c.659-61C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 1,572,630 control chromosomes in the GnomAD database, including 242,614 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 0.46 (18031 hom., cov: 32)
  • Exomes 𝑓: 0.56 (224583 hom.)
• Consequence: ADTRP NM_032744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 7 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032744.4. 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
	ADTRP	NM_032744.4	MANE Select	c.659-61C>T		intron	N/A	NP_116133.1
	ADTRP	NM_001143948.2		c.713-61C>T		intron	N/A	NP_001137420.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADTRP	ENST00000414691.8	TSL:1 MANE Select	c.659-61C>T		intron	N/A	ENSP00000404416.2
	ADTRP	ENST00000513651.5	TSL:1	n.384-61C>T		intron	N/A
	ADTRP	ENST00000229583.9	TSL:2	c.713-61C>T		intron	N/A	ENSP00000229583.5

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70625 AN: 151894 Hom.: 18027 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.485

GnomAD4 exome AF: 0.556 AC: 790484 AN: 1420618 Hom.: 224583 AF XY: 0.555 AC XY: 392415 AN XY: 707298

African (AFR) AF: 0.234 AC: 7268 AN: 31018

American (AMR) AF: 0.551 AC: 19667 AN: 35702

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 12584 AN: 24926

East Asian (EAS) AF: 0.321 AC: 12584 AN: 39256

South Asian (SAS) AF: 0.468 AC: 37545 AN: 80232

European-Finnish (FIN) AF: 0.468 AC: 24826 AN: 53018

Middle Eastern (MID) AF: 0.475 AC: 2676 AN: 5628

European-Non Finnish (NFE) AF: 0.589 AC: 642842 AN: 1092032

Other (OTH) AF: 0.519 AC: 30492 AN: 58806

GnomAD4 genome AF: 0.465 AC: 70650 AN: 152012 Hom.: 18031 Cov.: 32 AF XY: 0.458 AC XY: 34033 AN XY: 74308

African (AFR) AF: 0.257 AC: 10673 AN: 41478

American (AMR) AF: 0.526 AC: 8026 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1758 AN: 3472

East Asian (EAS) AF: 0.289 AC: 1494 AN: 5176

South Asian (SAS) AF: 0.461 AC: 2219 AN: 4814

European-Finnish (FIN) AF: 0.448 AC: 4724 AN: 10538

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.589 AC: 39997 AN: 67956

Other (OTH) AF: 0.483 AC: 1019 AN: 2108

Alfa AF: 0.547 Hom.: 84820

Bravo AF: 0.459

Asia WGS AF: 0.392 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.11
DANN	Benign	0.58
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3734273; hg19: chr6-11714806; COSMIC: COSV57643370; COSMIC: COSV57643370;