NM_001085457.2:c.445A>T

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

Scores

1
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.08
Variant links:
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]
FRG1HP (HGNC:51767): (FSHD region gene 1 family member H, pseudogene)

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
ZNG1FNM_001085457.2 linkc.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
ZNG1FENST00000377391.8 linkc.445A>T p.Met149Leu missense_variant Exon 5 of 15 1 NM_001085457.2 ENSP00000366608.4 Q4V339
ZNG1FENST00000456520.5 linkc.445A>T p.Met149Leu missense_variant Exon 5 of 14 1 ENSP00000401079.2 H0Y5V3
ZNG1FENST00000382436.7 linkn.313A>T non_coding_transcript_exon_variant Exon 5 of 16 1 ENSP00000484049.1 A0A087X1C0
ZNG1FENST00000467791.5 linkn.34A>T non_coding_transcript_exon_variant Exon 2 of 10 5 ENSP00000480830.1 A0A087WX94
ZNG1FENST00000486387.6 linkn.445A>T non_coding_transcript_exon_variant Exon 5 of 17 2 ENSP00000480837.1 A0A0B4J2E3

Frequencies

GnomAD3 genomes
Cov.:
26
GnomAD3 exomes
AF:
0.0000290
AC:
4
AN:
137716
Hom.:
0
AF XY:
0.0000261
AC XY:
2
AN XY:
76626
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000177
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000169
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1445208
Hom.:
0
Cov.:
36
AF XY:
0.00
AC XY:
0
AN XY:
718526
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_noAF
Benign
-0.35
CADD
Benign
20
DANN
Benign
0.77
DEOGEN2
Benign
0.0064
.;T;.;.
LIST_S2
Benign
0.82
T;T;D;D
MetaRNN
Uncertain
0.53
D;D;D;D
PROVEAN
Benign
-0.27
.;N;N;.
Sift
Benign
0.72
.;T;T;.
Sift4G
Benign
0.60
T;T;T;T
Vest4
0.65
gMVP
0.44

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs776177539; hg19: chr9-70871851; API