rs7753407

Variant names:

• chr6-11780108-G-A
• rs7753407
• ENST00000379415.6:c.-207-1142C>T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADTRP	ENST00000379415.6	c.-207-1142C>T		intron_variant	Intron 2 of 5	5		ENSP00000368726.2

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;