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

Variant summary

Our verdict is Benign. The variant received -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

Publications

6 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506810.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADTRP	ENST00000379415.6	TSL:5	c.-207-300A>G		intron	N/A	ENSP00000368726.2
	ADTRP	ENST00000506810.1	TSL:3	c.-208+257A>G		intron	N/A	ENSP00000422927.1

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

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.806

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.561

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.634

AC:

96470

AN:

152124

Hom.:

32941

Cov.:

AF XY:

0.628

AC XY:

46735

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.386

AC:

15988

AN:

41470

American (AMR)

AF:

0.713

AC:

10892

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.723

AC:

2510

AN:

3472

East Asian (EAS)

AF:

0.399

AC:

2068

AN:

5180

South Asian (SAS)

AF:

0.546

AC:

2629

AN:

4814

European-Finnish (FIN)

AF:

0.744

AC:

7879

AN:

10594

Middle Eastern (MID)

AF:

0.575

AC:

169

AN:

294

European-Non Finnish (NFE)

AF:

0.768

AC:

52195

AN:

67996

Other (OTH)

AF:

0.637

AC:

1347

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1565

3131

4696

6262

7827

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

766

1532

2298

3064

3830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.718

Hom.:

143129

Bravo

AF:

0.624

Asia WGS

AF:

0.466

AC:

1622

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.042

(source)

DANN

Benign

0.74

PhyloP100

-2.6

PromoterAI

0.072

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over