dbSNP rs2076188: ADTRP:c.-207-300A>G (chr6-11779266-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000506810.1(ADTRP):c.-208+257A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,214 control chromosomes in the GnomAD database, including 32,972 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 0.63 ( 32941 hom., cov: 32)

Exomes 𝑓: 0.81 ( 31 hom. )

Consequence

ADTRP
ENST00000506810.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.58

Variant links:

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]

ADTRP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.762 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 link	c.-207-300A>G		intron_variant	Intron 2 of 5	5		ENSP00000368726.2		D6R9A9
ADTRP	ENST00000506810.1 link	c.-208+257A>G		intron_variant	Intron 1 of 4	3		ENSP00000422927.1		D6R9A9

Frequencies

GnomAD3 genomes

AF:

0.634

AC:

96435

AN:

152008

Hom.:

32931

Cov.:

show subpopulations

Gnomad AFR

AF:

0.386

Gnomad AMI

AF:

0.870

Gnomad AMR

AF:

0.713

Gnomad ASJ

AF:

0.723

Gnomad EAS

AF:

0.400

Gnomad SAS

AF:

0.545

Gnomad FIN

AF:

0.744

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.768

Gnomad OTH

AF:

0.635

GnomAD4 exome

AF:

0.811

AC:

AN:

Hom.:

AF XY:

0.729

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.750

Gnomad4 NFE exome

AF:

0.806

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.634

AC:

96470

AN:

152124

Hom.:

32941

Cov.:

AF XY:

0.628

AC XY:

46735

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.386

Gnomad4 AMR

AF:

0.713

Gnomad4 ASJ

AF:

0.723

Gnomad4 EAS

AF:

0.399

Gnomad4 SAS

AF:

0.546

Gnomad4 FIN

AF:

0.744

Gnomad4 NFE

AF:

0.768

Gnomad4 OTH

AF:

0.637

Alfa

AF:

0.734

Hom.:

62757

Bravo

AF:

0.624

Asia WGS

AF:

0.466

AC:

1622

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.042

DANN

Benign

0.74

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over