rs17348507
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152491.5(PM20D1):c.257-50T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 1,491,854 control chromosomes in the GnomAD database, including 1,956 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 0.053 ( 285 hom., cov: 32)
Exomes 𝑓: 0.047 ( 1671 hom. )
Consequence
PM20D1
NM_152491.5 intron
NM_152491.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.665
Publications
3 publications found
Genes affected
PM20D1 (HGNC:26518): (peptidase M20 domain containing 1) Enables hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides. Involved in several processes, including amide biosynthetic process; cellular amide catabolic process; and negative regulation of neuron death. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.77).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0837 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0534 AC: 8127AN: 152162Hom.: 286 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
8127
AN:
152162
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0413 AC: 9601AN: 232434 AF XY: 0.0427 show subpopulations
GnomAD2 exomes
AF:
AC:
9601
AN:
232434
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0472 AC: 63162AN: 1339572Hom.: 1671 Cov.: 21 AF XY: 0.0476 AC XY: 31803AN XY: 668554 show subpopulations
GnomAD4 exome
AF:
AC:
63162
AN:
1339572
Hom.:
Cov.:
21
AF XY:
AC XY:
31803
AN XY:
668554
show subpopulations
African (AFR)
AF:
AC:
2846
AN:
30538
American (AMR)
AF:
AC:
819
AN:
41846
Ashkenazi Jewish (ASJ)
AF:
AC:
1322
AN:
24566
East Asian (EAS)
AF:
AC:
5
AN:
38832
South Asian (SAS)
AF:
AC:
4461
AN:
81418
European-Finnish (FIN)
AF:
AC:
1809
AN:
49606
Middle Eastern (MID)
AF:
AC:
414
AN:
5456
European-Non Finnish (NFE)
AF:
AC:
48831
AN:
1011168
Other (OTH)
AF:
AC:
2655
AN:
56142
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
2956
5912
8869
11825
14781
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
1860
3720
5580
7440
9300
<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: 0.0534 AC: 8137AN: 152282Hom.: 285 Cov.: 32 AF XY: 0.0521 AC XY: 3876AN XY: 74456 show subpopulations
GnomAD4 genome
AF:
AC:
8137
AN:
152282
Hom.:
Cov.:
32
AF XY:
AC XY:
3876
AN XY:
74456
show subpopulations
African (AFR)
AF:
AC:
3575
AN:
41532
American (AMR)
AF:
AC:
508
AN:
15308
Ashkenazi Jewish (ASJ)
AF:
AC:
203
AN:
3472
East Asian (EAS)
AF:
AC:
2
AN:
5188
South Asian (SAS)
AF:
AC:
237
AN:
4822
European-Finnish (FIN)
AF:
AC:
333
AN:
10616
Middle Eastern (MID)
AF:
AC:
19
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3160
AN:
68024
Other (OTH)
AF:
AC:
100
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
399
798
1196
1595
1994
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
94
188
282
376
470
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
84
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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