rs2893529

Positions:

• chr7-36360047-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199706.2(MATCAP2):​c.26-2457C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,222 control chromosomes in the GnomAD database, including 666 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 0.081 (666 hom., cov: 32)
• Consequence: MATCAP2 NM_001199706.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MATCAP2	NM_001199706.2	c.26-2457C>T		intron_variant		ENST00000440378.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MATCAP2	ENST00000440378.6	c.26-2457C>T		intron_variant		1	NM_001199706.2	P1

Frequencies

GnomAD3 genomes AF: 0.0808 AC: 12296 AN: 152104 Hom.: 662 Cov.: 32

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0809 AC: 12310 AN: 152222 Hom.: 666 Cov.: 32 AF XY: 0.0793 AC XY: 5901 AN XY: 74426

Gnomad4 AFR AF: 0.0220

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0336

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0725 Hom.: 80

Bravo AF: 0.0880

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.81

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

LitVar

Other links and lift over

dbSNP: rs2893529; hg19: chr7-36399656;