8-40674814-T-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024645.3(ZMAT4):āc.467A>Cā(p.Asn156Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,724 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 31)
Exomes š: 0.0000027 ( 0 hom. )
Consequence
ZMAT4
NM_024645.3 missense
NM_024645.3 missense
Scores
6
7
6
Clinical Significance
Conservation
PhyloP100: 7.62
Genes affected
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZMAT4 | NM_024645.3 | c.467A>C | p.Asn156Thr | missense_variant | 5/7 | ENST00000297737.11 | NP_078921.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZMAT4 | ENST00000297737.11 | c.467A>C | p.Asn156Thr | missense_variant | 5/7 | 2 | NM_024645.3 | ENSP00000297737 | P1 | |
ZMAT4 | ENST00000315769.11 | c.349+22431A>C | intron_variant | 1 | ENSP00000319785 | |||||
ZMAT4 | ENST00000519406.5 | c.467A>C | p.Asn156Thr | missense_variant | 5/6 | 3 | ENSP00000428423 | |||
ZMAT4 | ENST00000519806.1 | n.211A>C | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251106Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135702
GnomAD3 exomes
AF:
AC:
2
AN:
251106
Hom.:
AF XY:
AC XY:
2
AN XY:
135702
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 AF: 0.00000274 AC: 4AN: 1461724Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727166
GnomAD4 exome
AF:
AC:
4
AN:
1461724
Hom.:
Cov.:
31
AF XY:
AC XY:
4
AN XY:
727166
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.: 31
GnomAD4 genome
Cov.:
31
ExAC
AF:
AC:
1
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | The c.467A>C (p.N156T) alteration is located in exon 5 (coding exon 4) of the ZMAT4 gene. This alteration results from a A to C substitution at nucleotide position 467, causing the asparagine (N) at amino acid position 156 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;.
Polyphen
D;.
Vest4
MutPred
Gain of MoRF binding (P = 0.31);Gain of MoRF binding (P = 0.31);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
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