NM_001199706.2:c.26-2457C>T

Variant names:

• chr7-36360047-G-A
• rs2893529
• NM_001199706.2:c.26-2457C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MATCAP2	NM_001199706.2	MANE Select	c.26-2457C>T		intron	N/A	NP_001186635.1
	MATCAP2	NM_001100425.2		c.179-2457C>T		intron	N/A	NP_001093895.1
	MATCAP2	NM_001199707.2		c.140-2457C>T		intron	N/A	NP_001186636.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MATCAP2	ENST00000440378.6	TSL:1 MANE Select	c.26-2457C>T		intron	N/A	ENSP00000390837.1
	MATCAP2	ENST00000297063.10	TSL:1	c.179-2457C>T		intron	N/A	ENSP00000297063.6
	MATCAP2	ENST00000338533.9	TSL:1	c.140-2457C>T		intron	N/A	ENSP00000344805.5

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

African (AFR) AF: 0.0220 AC: 915 AN: 41546

American (AMR) AF: 0.143 AC: 2187 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3468

East Asian (EAS) AF: 0.156 AC: 806 AN: 5182

South Asian (SAS) AF: 0.123 AC: 592 AN: 4832

European-Finnish (FIN) AF: 0.0336 AC: 356 AN: 10594

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0958 AC: 6512 AN: 67996

Other (OTH) AF: 0.116 AC: 244 AN: 2112

Alfa AF: 0.0707 Hom.: 80

Bravo AF: 0.0880

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.81
PhyloP100		0.018
Mutation Taster		=100/0	polymorphism (auto)

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

dbSNP: rs2893529; hg19: chr7-36399656;