NM_001394560.1:c.1488G>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001394560.1(ZMAT1):​c.1488G>A​(p.Met496Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000166 in 1,207,848 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

Frequency

Genomes: 𝑓 0.0000089 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 9.1e-7 ( 0 hom. 0 hem. )

Consequence

ZMAT1
NM_001394560.1 missense

Scores

14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.250
Variant links:
Genes affected
ZMAT1 (HGNC:29377): (zinc finger matrin-type 1) This gene encodes a protein containing Cys2-His2 (C2H2)-type zinc fingers, which are similar to those found in the nuclear matrix protein matrin 3. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08139947).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZMAT1NM_001394560.1 linkc.1488G>A p.Met496Ile missense_variant Exon 6 of 6 ENST00000651725.2 NP_001381489.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZMAT1ENST00000651725.2 linkc.1488G>A p.Met496Ile missense_variant Exon 6 of 6 NM_001394560.1 ENSP00000498446.1 A0A494C0A7

Frequencies

GnomAD3 genomes
AF:
0.00000892
AC:
1
AN:
112167
Hom.:
0
Cov.:
23
AF XY:
0.0000291
AC XY:
1
AN XY:
34387
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000188
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000553
AC:
1
AN:
180717
Hom.:
0
AF XY:
0.0000151
AC XY:
1
AN XY:
66041
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000123
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
9.13e-7
AC:
1
AN:
1095681
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
362017
show subpopulations
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:
0.0000185
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000892
AC:
1
AN:
112167
Hom.:
0
Cov.:
23
AF XY:
0.0000291
AC XY:
1
AN XY:
34387
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000188
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.0000165
AC:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.30
BayesDel_addAF
Benign
-0.41
T
BayesDel_noAF
Benign
-0.83
CADD
Benign
4.5
DANN
Benign
0.69
FATHMM_MKL
Benign
0.027
N
M_CAP
Benign
0.053
D
MetaRNN
Benign
0.081
T;T
MetaSVM
Benign
-1.1
T
PrimateAI
Benign
0.37
T
PROVEAN
Benign
-2.2
N;N
REVEL
Benign
0.011
Sift
Benign
0.10
T;T
Sift4G
Benign
0.14
T;T
Vest4
0.10
MutPred
0.33
Loss of catalytic residue at M439 (P = 0.0418);Loss of catalytic residue at M439 (P = 0.0418);
MVP
0.26
MPC
0.10
ClinPred
0.067
T
GERP RS
-0.41
gMVP
0.10

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: rs771282199; hg19: chrX-101139082; API