rs197328

Variant names:

• chr7-36356749-G-A
• rs197328
• ENST00000415803.2:c.*66C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415803.2(MATCAP2):​c.*66C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 688,556 control chromosomes in the GnomAD database, including 79,821 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 0.43 (15028 hom., cov: 32)
  • Exomes 𝑓: 0.48 (64793 hom.)
• Consequence: MATCAP2 ENST00000415803.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MATCAP2	NM_001199706.2	c.714+153C>T		intron_variant	Intron 2 of 6	ENST00000440378.6	NP_001186635.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MATCAP2	ENST00000440378.6	c.714+153C>T		intron_variant	Intron 2 of 6	1	NM_001199706.2	ENSP00000390837.1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65466 AN: 151922 Hom.: 15024 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.402

GnomAD4 exome AF: 0.485 AC: 260141 AN: 536516 Hom.: 64793 Cov.: 6 AF XY: 0.493 AC XY: 140339 AN XY: 284784

African (AFR) AF: 0.284 AC: 4162 AN: 14652

American (AMR) AF: 0.522 AC: 14496 AN: 27768

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 7821 AN: 16274

East Asian (EAS) AF: 0.528 AC: 16785 AN: 31778

South Asian (SAS) AF: 0.636 AC: 34168 AN: 53746

European-Finnish (FIN) AF: 0.594 AC: 20628 AN: 34740

Middle Eastern (MID) AF: 0.475 AC: 1513 AN: 3188

European-Non Finnish (NFE) AF: 0.452 AC: 146967 AN: 325060

Other (OTH) AF: 0.464 AC: 13601 AN: 29310

GnomAD4 genome AF: 0.431 AC: 65505 AN: 152040 Hom.: 15028 Cov.: 32 AF XY: 0.447 AC XY: 33217 AN XY: 74338

African (AFR) AF: 0.282 AC: 11707 AN: 41446

American (AMR) AF: 0.499 AC: 7618 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3470

East Asian (EAS) AF: 0.529 AC: 2737 AN: 5172

South Asian (SAS) AF: 0.631 AC: 3045 AN: 4822

European-Finnish (FIN) AF: 0.626 AC: 6612 AN: 10566

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30604 AN: 67972

Other (OTH) AF: 0.403 AC: 851 AN: 2114

Alfa AF: 0.444 Hom.: 66755

Bravo AF: 0.409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.050
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: rs197328; hg19: chr7-36396358;