chr7-36357131-G-A

Variant names:

• chr7-36357131-G-A
• NM_001199706.2:c.485C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001199706.2(MATCAP2):​c.485C>T​(p.Thr162Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MATCAP2 NM_001199706.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.51
• Publications: 0 publications found

Genes affected

MATCAP2 (HGNC:22206): (microtubule associated tyrosine carboxypeptidase 2)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.061974734).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199706.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MATCAP2	NM_001199706.2	MANE Select	c.485C>T	p.Thr162Ile	missense	Exon 2 of 7	NP_001186635.1	Q8NCT3-6
	MATCAP2	NM_001100425.2		c.638C>T	p.Thr213Ile	missense	Exon 3 of 7	NP_001093895.1	Q8NCT3-1
	MATCAP2	NM_001199707.2		c.599C>T	p.Thr200Ile	missense	Exon 2 of 6	NP_001186636.1	Q8NCT3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MATCAP2	ENST00000440378.6	TSL:1 MANE Select	c.485C>T	p.Thr162Ile	missense	Exon 2 of 7	ENSP00000390837.1	Q8NCT3-6
	MATCAP2	ENST00000297063.10	TSL:1	c.638C>T	p.Thr213Ile	missense	Exon 3 of 7	ENSP00000297063.6	Q8NCT3-1
	MATCAP2	ENST00000338533.9	TSL:1	c.599C>T	p.Thr200Ile	missense	Exon 2 of 6	ENSP00000344805.5	Q8NCT3-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	16
DANN	Benign	0.97
DEOGEN2	Benign	0.057	T
Eigen	Benign	-0.61
Eigen_PC	Benign	-0.57
FATHMM_MKL	Benign	0.23	N
LIST_S2	Benign	0.77	T
M_CAP	Benign	0.0051	T
MetaRNN	Benign	0.062	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.69	N
PhyloP100		1.5
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-1.9	N
REVEL	Benign	0.071
Sift	Benign	0.038	D
Sift4G	Uncertain	0.052	T
Polyphen		0.035	B
Vest4		0.11
MutPred		0.18		Gain of catalytic residue at P215 (P = 0.0375)
MVP		0.12
MPC		0.34
ClinPred		0.15	T
GERP RS		4.8
Varity_R		0.046
gMVP		0.25
Mutation Taster		=96/4	polymorphism

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

Other links and lift over

hg19: chr7-36396740;