NM_001085457.2:c.445A>T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001085457.2(ZNG1F):c.445A>T(p.Met149Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M149V) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 26)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ZNG1F
NM_001085457.2 missense
NM_001085457.2 missense
Scores
1
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.08
Genes affected
ZNG1F (HGNC:31978): (Zn regulated GTPase metalloprotein activator 1F) Predicted to enable ATP binding activity. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 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 |
---|---|---|---|---|---|---|---|---|
ZNG1F | NM_001085457.2 | c.445A>T | p.Met149Leu | missense_variant | Exon 5 of 15 | ENST00000377391.8 | NP_001078926.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNG1F | ENST00000377391.8 | c.445A>T | p.Met149Leu | missense_variant | Exon 5 of 15 | 1 | NM_001085457.2 | ENSP00000366608.4 | ||
ZNG1F | ENST00000456520.5 | c.445A>T | p.Met149Leu | missense_variant | Exon 5 of 14 | 1 | ENSP00000401079.2 | |||
ZNG1F | ENST00000382436.7 | n.313A>T | non_coding_transcript_exon_variant | Exon 5 of 16 | 1 | ENSP00000484049.1 | ||||
ZNG1F | ENST00000467791.5 | n.34A>T | non_coding_transcript_exon_variant | Exon 2 of 10 | 5 | ENSP00000480830.1 | ||||
ZNG1F | ENST00000486387.6 | n.445A>T | non_coding_transcript_exon_variant | Exon 5 of 17 | 2 | ENSP00000480837.1 |
Frequencies
GnomAD3 genomes Cov.: 26
GnomAD3 genomes
Cov.:
26
GnomAD3 exomes AF: 0.0000290 AC: 4AN: 137716Hom.: 0 AF XY: 0.0000261 AC XY: 2AN XY: 76626
GnomAD3 exomes
AF:
AC:
4
AN:
137716
Hom.:
AF XY:
AC XY:
2
AN XY:
76626
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1445208Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 718526
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1445208
Hom.:
Cov.:
36
AF XY:
AC XY:
0
AN XY:
718526
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 26
GnomAD4 genome
Cov.:
26
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
.;T;.;.
LIST_S2
Benign
T;T;D;D
MetaRNN
Uncertain
D;D;D;D
PROVEAN
Benign
.;N;N;.
Sift
Benign
.;T;T;.
Sift4G
Benign
T;T;T;T
Vest4
gMVP
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