Genetic Variant ADTRP:c.-96G>A (chr6-11778855-C-T) – 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.-96G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 1,362,502 control chromosomes in the GnomAD database, including 99,816 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 0.39 ( 11752 hom., cov: 32)

Exomes 𝑓: 0.38 ( 88064 hom. )

Consequence

ADTRP
ENST00000506810.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.628

Publications

11 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:

Genome browser will be placed here

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=-0.77).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 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
	ADTRP	NM_032744.4	MANE Select	c.-96G>A		upstream_gene	N/A	NP_116133.1
	ADTRP	NM_001143948.2		c.-96G>A		upstream_gene	N/A	NP_001137420.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ADTRP	ENST00000379415.6	TSL:5	c.-96G>A	5_prime_UTR	Exon 3 of 6	ENSP00000368726.2
ADTRP	ENST00000506810.1	TSL:3	c.-96G>A	5_prime_UTR	Exon 2 of 5	ENSP00000422927.1
ADTRP	ENST00000414691.8	TSL:1 MANE Select	c.-96G>A	upstream_gene	N/A	ENSP00000404416.2

Frequencies

GnomAD3 genomes

AF:

0.388

AC:

59018

AN:

151942

Hom.:

11735

Cov.:

show subpopulations

Gnomad AFR

AF:

0.445

Gnomad AMI

AF:

0.292

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.384

Gnomad EAS

AF:

0.217

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.389

GnomAD4 exome

AF:

0.381

AC:

461075

AN:

1210442

Hom.:

88064

Cov.:

AF XY:

0.377

AC XY:

226006

AN XY:

599560

show subpopulations

African (AFR)

AF:

0.453

AC:

12546

AN:

27690

American (AMR)

AF:

0.327

AC:

10372

AN:

31750

Ashkenazi Jewish (ASJ)

AF:

0.378

AC:

7609

AN:

20104

East Asian (EAS)

AF:

0.219

AC:

8098

AN:

36918

South Asian (SAS)

AF:

0.283

AC:

18207

AN:

64446

European-Finnish (FIN)

AF:

0.439

AC:

21533

AN:

49086

Middle Eastern (MID)

AF:

0.349

AC:

1340

AN:

3838

European-Non Finnish (NFE)

AF:

0.391

AC:

362180

AN:

925778

Other (OTH)

AF:

0.378

AC:

19190

AN:

50832

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

13477

26954

40430

53907

67384

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11324

22648

33972

45296

56620

<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:

0.388

AC:

59070

AN:

152060

Hom.:

11752

Cov.:

AF XY:

0.385

AC XY:

28597

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.445

AC:

18437

AN:

41458

American (AMR)

AF:

0.352

AC:

5380

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.384

AC:

1331

AN:

3468

East Asian (EAS)

AF:

0.217

AC:

1125

AN:

5188

South Asian (SAS)

AF:

0.280

AC:

1350

AN:

4822

European-Finnish (FIN)

AF:

0.428

AC:

4524

AN:

10568

Middle Eastern (MID)

AF:

0.381

AC:

112

AN:

294

European-Non Finnish (NFE)

AF:

0.379

AC:

25727

AN:

67960

Other (OTH)

AF:

0.387

AC:

818

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1857

3713

5570

7426

9283

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

560

1120

1680

2240

2800

<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:

0.377

Hom.:

35260

Bravo

AF:

0.389

Asia WGS

AF:

0.270

AC:

941

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.058

(source)

DANN

Benign

0.67

PhyloP100

-0.63

PromoterAI

0.013

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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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