GeneBe

chr6-11714661-GA-G

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_032744.4(ADTRP):​c.659-150delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000144 in 693,462 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

ADTRP
NM_032744.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.698

Publications

0 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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADTRPNM_032744.4 linkc.659-150delT intron_variant Intron 5 of 5 ENST00000414691.8 NP_116133.1 Q96IZ2-1
ADTRPNM_001143948.2 linkc.713-150delT intron_variant Intron 6 of 6 NP_001137420.1 Q96IZ2-2
ADTRPXM_011514956.2 linkc.765-150delT intron_variant Intron 6 of 6 XP_011513258.1 Q96IZ2-3
ADTRPXM_047419420.1 linkc.378-150delT intron_variant Intron 6 of 6 XP_047275376.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ADTRPENST00000414691.8 linkc.659-150delT intron_variant Intron 5 of 5 1 NM_032744.4 ENSP00000404416.2 Q96IZ2-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.00000144
AC:
1
AN:
693462
Hom.:
0
AF XY:
0.00000280
AC XY:
1
AN XY:
357238
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.0000629
AC:
1
AN:
15904
American (AMR)
AF:
0.00
AC:
0
AN:
19180
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15598
East Asian (EAS)
AF:
0.00
AC:
0
AN:
30746
South Asian (SAS)
AF:
0.00
AC:
0
AN:
47950
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
45590
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3780
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
481120
Other (OTH)
AF:
0.00
AC:
0
AN:
33594
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.70

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

Other links and lift over

dbSNP: rs80355771; hg19: chr6-11714894; API