7-36357326-T-G

Variant summary

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

The NM_001199706.2(MATCAP2):​c.290A>C​(p.Asp97Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

MATCAP2
NM_001199706.2 missense

Scores

1
3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.06
Variant links:
Genes affected
MATCAP2 (HGNC:22206): (microtubule associated tyrosine carboxypeptidase 2)

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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=0.17128074).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MATCAP2NM_001199706.2 linkc.290A>C p.Asp97Ala missense_variant Exon 2 of 7 ENST00000440378.6 NP_001186635.1 Q8NCT3-6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MATCAP2ENST00000440378.6 linkc.290A>C p.Asp97Ala missense_variant Exon 2 of 7 1 NM_001199706.2 ENSP00000390837.1 Q8NCT3-6

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461874
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
727236
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:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Benign
-0.10
T
BayesDel_noAF
Benign
-0.39
CADD
Benign
19
DANN
Uncertain
0.98
DEOGEN2
Benign
0.049
T;.;.;.;.
Eigen
Benign
0.086
Eigen_PC
Benign
0.15
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.76
T;T;T;T;T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.17
T;T;T;T;T
MetaSVM
Benign
-0.74
T
MutationAssessor
Benign
2.0
M;.;.;.;.
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-1.8
N;N;N;N;N
REVEL
Benign
0.20
Sift
Uncertain
0.0060
D;D;D;T;T
Sift4G
Uncertain
0.040
D;D;T;T;D
Polyphen
0.43
B;B;B;.;P
Vest4
0.17
MutPred
0.18
Gain of MoRF binding (P = 0.1037);.;.;.;.;
MVP
0.44
MPC
0.59
ClinPred
0.77
D
GERP RS
5.7
Varity_R
0.15
gMVP
0.20

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-36396935; API