Variant 7-36387852-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

Variant links:

Genes affected

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

MATCAP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MATCAP2	NM_001100425.2 link	c.108+2115A>G		intron_variant			NP_001093895.1	Q8NCT3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MATCAP2	ENST00000297063.10 link	c.108+2115A>G		intron_variant		1		ENSP00000297063.6		Q8NCT3-1
MATCAP2	ENST00000429651.1 link	c.108+2115A>G		intron_variant		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

Gnomad4 AFR

AF:

0.512

Gnomad4 AMR

AF:

0.325

Gnomad4 ASJ

AF:

0.349

Gnomad4 EAS

AF:

0.284

Gnomad4 SAS

AF:

0.225

Gnomad4 FIN

AF:

0.280

Gnomad4 NFE

AF:

0.426

Gnomad4 OTH

AF:

0.427

Alfa

AF:

0.417

Hom.:

27324

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

DANN

Benign

0.94

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over