6-11774559-C-T

Position:

• chr6-11774559-C-T

Variant summary

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

The NM_032744.4(ADTRP):​c.153+4048G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,248 control chromosomes in the GnomAD database, including 38,022 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 0.70 (38022 hom., cov: 27)
• Consequence: ADTRP NM_032744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADTRP	NM_032744.4	c.153+4048G>A		intron_variant		ENST00000414691.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADTRP	ENST00000414691.8	c.153+4048G>A		intron_variant		1	NM_032744.4	P1

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106200 AN: 151128 Hom.: 37974 Cov.: 27

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.644

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.703 AC: 106306 AN: 151248 Hom.: 38022 Cov.: 27 AF XY: 0.713 AC XY: 52661 AN XY: 73882

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.688

Alfa AF: 0.629 Hom.: 41606

Bravo AF: 0.705

Asia WGS AF: 0.854 AC: 2968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.53

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: rs6929400; hg19: chr6-11774792;