ENST00000297063.10:c.108+2115A>G

Variant names:

• chr7-36387852-T-C
• rs6976779
• ENST00000297063.10:c.108+2115A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000297063.10(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 ENST00000297063.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 3 publications found

Genes affected

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

ACMG classification

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	c.108+2115A>G		intron_variant	Intron 1 of 6		NP_001093895.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63133 AN: 151876 Hom.: 13670 Cov.: 31

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.: 31 AF XY: 0.401 AC XY: 29814 AN XY: 74312

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

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	18
DANN	Benign	0.94
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6976779; hg19: chr7-36427461; COSMIC: COSV51710274; COSMIC: COSV51710274;