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:

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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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032744.4. 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.659-150dupT		intron	N/A	NP_116133.1	Q96IZ2-1
	ADTRP	NM_001143948.2		c.713-150dupT		intron	N/A	NP_001137420.1	Q96IZ2-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADTRP	ENST00000414691.8	TSL:1 MANE Select	c.659-150_659-149insT	intron	N/A	ENSP00000404416.2	Q96IZ2-1
ADTRP	ENST00000513651.5	TSL:1	n.384-150_384-149insT	intron	N/A
ADTRP	ENST00000894491.1		c.809-150_809-149insT	intron	N/A	ENSP00000564550.1

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 v4.9

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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6-11714661-GA-GAA

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