rs7753407

Positions:

• chr6-11780108-G-A

Variant summary

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

The ENST00000379415.6(ADTRP):​c.-207-1142C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 151,478 control chromosomes in the GnomAD database, including 43,851 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 0.75 (43851 hom., cov: 27)
• Consequence: ADTRP ENST00000379415.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADTRP	ENST00000379415.6	c.-207-1142C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113438 AN: 151366 Hom.: 43839 Cov.: 27

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.749 AC: 113484 AN: 151478 Hom.: 43851 Cov.: 27 AF XY: 0.745 AC XY: 55169 AN XY: 74012

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.758

Alfa AF: 0.807 Hom.: 10809

Bravo AF: 0.739

Asia WGS AF: 0.592 AC: 2059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7753407; hg19: chr6-11780341;