6-11714573-G-A

Position:

• chr6-11714573-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ADTRP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADTRP	NM_032744.4	c.659-61C>T		intron_variant		ENST00000414691.8	NP_116133.1
ADTRP	NM_001143948.2	c.713-61C>T		intron_variant			NP_001137420.1
ADTRP	XM_011514956.2	c.765-61C>T		intron_variant			XP_011513258.1
ADTRP	XM_047419420.1	c.378-61C>T		intron_variant			XP_047275376.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADTRP	ENST00000414691.8	c.659-61C>T		intron_variant		1	NM_032744.4	ENSP00000404416.2

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

Gnomad4 AFR exome AF: 0.234

Gnomad4 AMR exome AF: 0.551

Gnomad4 ASJ exome AF: 0.505

Gnomad4 EAS exome AF: 0.321

Gnomad4 SAS exome AF: 0.468

Gnomad4 FIN exome AF: 0.468

Gnomad4 NFE exome AF: 0.589

Gnomad4 OTH exome AF: 0.519

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

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.483

Alfa AF: 0.562 Hom.: 36155

Bravo AF: 0.459

Asia WGS AF: 0.392 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.11
DANN	Benign	0.58

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

Publications

LitVar

Other links and lift over

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