6-11778855-C-T

Variant names:

• chr6-11778855-C-T
• rs2076189
• ENST00000379415.6:c.-96G>A

Variant summary

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

The ENST00000379415.6(ADTRP):​c.-96G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 1,362,502 control chromosomes in the GnomAD database, including 99,816 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 0.39 (11752 hom., cov: 32)
  • Exomes 𝑓: 0.38 (88064 hom.)
• Consequence: ADTRP ENST00000379415.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628
• Publications: 11 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADTRP	NM_032744.4	c.-96G>A		upstream_gene_variant		ENST00000414691.8	NP_116133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADTRP	ENST00000414691.8	c.-96G>A		upstream_gene_variant		1	NM_032744.4	ENSP00000404416.2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 59018 AN: 151942 Hom.: 11735 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.389

GnomAD4 exome AF: 0.381 AC: 461075 AN: 1210442 Hom.: 88064 Cov.: 15 AF XY: 0.377 AC XY: 226006 AN XY: 599560

African (AFR) AF: 0.453 AC: 12546 AN: 27690

American (AMR) AF: 0.327 AC: 10372 AN: 31750

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 7609 AN: 20104

East Asian (EAS) AF: 0.219 AC: 8098 AN: 36918

South Asian (SAS) AF: 0.283 AC: 18207 AN: 64446

European-Finnish (FIN) AF: 0.439 AC: 21533 AN: 49086

Middle Eastern (MID) AF: 0.349 AC: 1340 AN: 3838

European-Non Finnish (NFE) AF: 0.391 AC: 362180 AN: 925778

Other (OTH) AF: 0.378 AC: 19190 AN: 50832

GnomAD4 genome AF: 0.388 AC: 59070 AN: 152060 Hom.: 11752 Cov.: 32 AF XY: 0.385 AC XY: 28597 AN XY: 74318

African (AFR) AF: 0.445 AC: 18437 AN: 41458

American (AMR) AF: 0.352 AC: 5380 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3468

East Asian (EAS) AF: 0.217 AC: 1125 AN: 5188

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4822

European-Finnish (FIN) AF: 0.428 AC: 4524 AN: 10568

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25727 AN: 67960

Other (OTH) AF: 0.387 AC: 818 AN: 2112

Alfa AF: 0.377 Hom.: 35260

Bravo AF: 0.389

Asia WGS AF: 0.270 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.058
DANN	Benign	0.67
PhyloP100		-0.63
PromoterAI		0.013	Neutral
Mutation Taster		=300/0	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: rs2076189; hg19: chr6-11779088; COSMIC: COSV57645449; COSMIC: COSV57645449;