Genetic Variant ADTRP:c.659-150dupT (chr6-11714661-G-GA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_032744.4(ADTRP):c.659-150dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0529 in 845,424 control chromosomes in the GnomAD database, including 4,339 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.063 ( 820 hom., cov: 31)

Exomes 𝑓: 0.051 ( 3519 hom. )

Consequence

ADTRP
NM_032744.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.698

Publications

1 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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ADTRP	NM_032744.4 link	c.659-150dupT	intron_variant	Intron 5 of 5	ENST00000414691.8	NP_116133.1	Q96IZ2-1
ADTRP	NM_001143948.2 link	c.713-150dupT	intron_variant	Intron 6 of 6		NP_001137420.1	Q96IZ2-2
ADTRP	XM_011514956.2 link	c.765-150dupT	intron_variant	Intron 6 of 6		XP_011513258.1	Q96IZ2-3
ADTRP	XM_047419420.1 link	c.378-150dupT	intron_variant	Intron 6 of 6		XP_047275376.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADTRP	ENST00000414691.8 link	c.659-150_659-149insT		intron_variant	Intron 5 of 5	1	NM_032744.4	ENSP00000404416.2		Q96IZ2-1

Frequencies

GnomAD3 genomes

AF:

0.0626

AC:

9526

AN:

152098

Hom.:

820

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0694

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0413

Gnomad ASJ

AF:

0.0775

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.0601

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0276

Gnomad OTH

AF:

0.0521

GnomAD4 exome

AF:

0.0508

AC:

35186

AN:

693206

Hom.:

3519

AF XY:

0.0526

AC XY:

18780

AN XY:

357072

show subpopulations

African (AFR)

AF:

0.0578

AC:

918

AN:

15894

American (AMR)

AF:

0.0334

AC:

640

AN:

19174

Ashkenazi Jewish (ASJ)

AF:

0.0701

AC:

1093

AN:

15594

East Asian (EAS)

AF:

0.409

AC:

12560

AN:

30680

South Asian (SAS)

AF:

0.106

AC:

5094

AN:

47904

European-Finnish (FIN)

AF:

0.0554

AC:

2526

AN:

45572

Middle Eastern (MID)

AF:

0.0672

AC:

254

AN:

3778

European-Non Finnish (NFE)

AF:

0.0209

AC:

10065

AN:

481032

Other (OTH)

AF:

0.0606

AC:

2036

AN:

33578

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1347

2694

4040

5387

6734

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

328

656

984

1312

1640

<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:

0.0626

AC:

9535

AN:

152218

Hom.:

820

Cov.:

AF XY:

0.0675

AC XY:

5021

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0693

AC:

2880

AN:

41536

American (AMR)

AF:

0.0413

AC:

632

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0775

AC:

269

AN:

3470

East Asian (EAS)

AF:

0.470

AC:

2424

AN:

5152

South Asian (SAS)

AF:

0.140

AC:

674

AN:

4820

European-Finnish (FIN)

AF:

0.0601

AC:

637

AN:

10604

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0276

AC:

1877

AN:

68024

Other (OTH)

AF:

0.0553

AC:

117

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

384

768

1153

1537

1921

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0427

Hom.:

Bravo

AF:

0.0623

Asia WGS

AF:

0.270

AC:

937

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.70

Mutation Taster

=100/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over