Genetic Variant MATCAP2:c.108+2115A>G (chr7-36387852-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001100425.2(MATCAP2):c.108+2115A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,994 control chromosomes in the GnomAD database, including 13,662 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.42 ( 13662 hom., cov: 31)

Consequence

MATCAP2
NM_001100425.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.177

Publications

3 publications found

Variant links:

Genes affected

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

MATCAP2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MATCAP2	NM_001100425.2 link	c.108+2115A>G		intron_variant	Intron 1 of 6		NP_001093895.1	Q8NCT3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MATCAP2	ENST00000297063.10 link	c.108+2115A>G		intron_variant	Intron 1 of 6	1		ENSP00000297063.6		Q8NCT3-1
MATCAP2	ENST00000429651.1 link	c.108+2115A>G		intron_variant	Intron 1 of 2	3		ENSP00000390527.1		C9JGM1

Frequencies

GnomAD3 genomes

AF:

0.416

AC:

63133

AN:

151876

Hom.:

13670

Cov.:

show subpopulations

Gnomad AFR

AF:

0.512

Gnomad AMI

AF:

0.317

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.280

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.426

Gnomad OTH

AF:

0.430

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.415

AC:

63141

AN:

151994

Hom.:

13662

Cov.:

AF XY:

0.401

AC XY:

29814

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.512

AC:

21191

AN:

41428

American (AMR)

AF:

0.325

AC:

4960

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.349

AC:

1209

AN:

3466

East Asian (EAS)

AF:

0.284

AC:

1469

AN:

5174

South Asian (SAS)

AF:

0.225

AC:

1086

AN:

4822

European-Finnish (FIN)

AF:

0.280

AC:

2964

AN:

10572

Middle Eastern (MID)

AF:

0.404

AC:

118

AN:

292

European-Non Finnish (NFE)

AF:

0.426

AC:

28952

AN:

67948

Other (OTH)

AF:

0.427

AC:

903

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1851

3702

5552

7403

9254

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.421

Hom.:

41689

Bravo

AF:

0.427

Asia WGS

AF:

0.258

AC:

900

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

(source)

DANN

Benign

0.94

PhyloP100

0.18

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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7-36387852-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over