GeneBe

chr16-72190436-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_047434734.1(PMFBP1):​c.-863+9964G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,098 control chromosomes in the GnomAD database, including 23,020 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 0.55 ( 23020 hom., cov: 33)

Consequence

PMFBP1
XM_047434734.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.133

Publications

17 publications found
Variant links:
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 31
    Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

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 (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PMFBP1XM_047434734.1 linkc.-863+9964G>A intron_variant Intron 3 of 23 XP_047290690.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.546
AC:
83031
AN:
151980
Hom.:
22995
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.607
Gnomad AMI
AF:
0.399
Gnomad AMR
AF:
0.443
Gnomad ASJ
AF:
0.677
Gnomad EAS
AF:
0.339
Gnomad SAS
AF:
0.638
Gnomad FIN
AF:
0.536
Gnomad MID
AF:
0.586
Gnomad NFE
AF:
0.538
Gnomad OTH
AF:
0.545
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.546
AC:
83103
AN:
152098
Hom.:
23020
Cov.:
33
AF XY:
0.544
AC XY:
40448
AN XY:
74354
show subpopulations
African (AFR)
AF:
0.608
AC:
25199
AN:
41478
American (AMR)
AF:
0.443
AC:
6767
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.677
AC:
2351
AN:
3472
East Asian (EAS)
AF:
0.339
AC:
1751
AN:
5168
South Asian (SAS)
AF:
0.637
AC:
3076
AN:
4830
European-Finnish (FIN)
AF:
0.536
AC:
5663
AN:
10564
Middle Eastern (MID)
AF:
0.582
AC:
170
AN:
292
European-Non Finnish (NFE)
AF:
0.538
AC:
36613
AN:
67996
Other (OTH)
AF:
0.544
AC:
1149
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1935
3870
5804
7739
9674
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
730
1460
2190
2920
3650
<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:
0.539
Hom.:
12500
Bravo
AF:
0.537
Asia WGS
AF:
0.505
AC:
1760
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
6.2
DANN
Benign
0.65
PhyloP100
0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12918956; hg19: chr16-72224335; API