NM_031293.3:c.166-1246T>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_031293.3(PMFBP1):c.166-1246T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.069 in 152,292 control chromosomes in the GnomAD database, including 451 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 0.069 ( 451 hom., cov: 32)
Consequence
PMFBP1
NM_031293.3 intron
NM_031293.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.03
Publications
3 publications found
Genes affected
PMFBP1 (HGNC:17728): (polyamine modulated factor 1 binding protein 1) Involved in spermatogenesis. Located in sperm connecting piece. Implicated in spermatogenic failure 31. [provided by Alliance of Genome Resources, Apr 2022]
PMFBP1 Gene-Disease associations (from GenCC):
- spermatogenic failure 31Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
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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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0963 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0691 AC: 10520AN: 152174Hom.: 452 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
10520
AN:
152174
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0690 AC: 10515AN: 152292Hom.: 451 Cov.: 32 AF XY: 0.0656 AC XY: 4887AN XY: 74480 show subpopulations
GnomAD4 genome
AF:
AC:
10515
AN:
152292
Hom.:
Cov.:
32
AF XY:
AC XY:
4887
AN XY:
74480
show subpopulations
African (AFR)
AF:
AC:
1337
AN:
41570
American (AMR)
AF:
AC:
994
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
281
AN:
3472
East Asian (EAS)
AF:
AC:
236
AN:
5186
South Asian (SAS)
AF:
AC:
197
AN:
4828
European-Finnish (FIN)
AF:
AC:
591
AN:
10616
Middle Eastern (MID)
AF:
AC:
26
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6681
AN:
68016
Other (OTH)
AF:
AC:
143
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
510
1020
1530
2040
2550
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
128
256
384
512
640
<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:
183
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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