NM_032744.4:c.390+3156A>C

Variant names:

• chr6-11763118-T-G
• rs2235394
• NM_032744.4:c.390+3156A>C

Variant summary

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

The NM_032744.4(ADTRP):​c.390+3156A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,112 control chromosomes in the GnomAD database, including 27,601 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 0.60 (27601 hom., cov: 33)
• Consequence: ADTRP NM_032744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADTRP	NM_032744.4	c.390+3156A>C		intron_variant	Intron 3 of 5	ENST00000414691.8	NP_116133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADTRP	ENST00000414691.8	c.390+3156A>C		intron_variant	Intron 3 of 5	1	NM_032744.4	ENSP00000404416.2

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91391 AN: 151994 Hom.: 27589 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.601 AC: 91442 AN: 152112 Hom.: 27601 Cov.: 33 AF XY: 0.596 AC XY: 44345 AN XY: 74362

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.605

Alfa AF: 0.561 Hom.: 4127

Bravo AF: 0.607

Asia WGS AF: 0.506 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.76

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: rs2235394; hg19: chr6-11763351;