rs197328

Positions:

• chr7-36356749-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• 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/exons	MANE	UniProt
MATCAP2	NM_001199706.2	c.714+153C>T		intron_variant		ENST00000440378.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MATCAP2	ENST00000440378.6	c.714+153C>T		intron_variant		1	NM_001199706.2	P1

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

Gnomad4 AFR exome AF: 0.284

Gnomad4 AMR exome AF: 0.522

Gnomad4 ASJ exome AF: 0.481

Gnomad4 EAS exome AF: 0.528

Gnomad4 SAS exome AF: 0.636

Gnomad4 FIN exome AF: 0.594

Gnomad4 NFE exome AF: 0.452

Gnomad4 OTH exome AF: 0.464

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

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.403

Alfa AF: 0.451 Hom.: 31517

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

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: rs197328; hg19: chr7-36396358;