7-36389691-G-A

Position:

• chr7-36389691-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The ENST00000297063.10(MATCAP2):​c.108+276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0241 in 261,268 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.021 (51 hom., cov: 33)
  • Exomes 𝑓: 0.029 (54 hom.)
• Consequence: MATCAP2 ENST00000297063.10 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.22

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 7-36389691-G-A is Benign according to our data. Variant chr7-36389691-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1201038.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0205 (3122/152266) while in subpopulation NFE AF= 0.0302 (2053/67998). AF 95% confidence interval is 0.0291. There are 51 homozygotes in gnomad4. There are 1414 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 51 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MATCAP2	NM_001100425.2	c.108+276C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MATCAP2	ENST00000297063.10	c.108+276C>T		intron_variant		1
MATCAP2	ENST00000429651.1	c.108+276C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3124 AN: 152154 Hom.: 51 Cov.: 33

Gnomad AFR AF: 0.00531

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0238

Gnomad ASJ AF: 0.0734

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0302

Gnomad OTH AF: 0.0301

GnomAD4 exome AF: 0.0292 AC: 3180 AN: 109002 Hom.: 54 AF XY: 0.0287 AC XY: 1592 AN XY: 55510

Gnomad4 AFR exome AF: 0.00678

Gnomad4 AMR exome AF: 0.0270

Gnomad4 ASJ exome AF: 0.0753

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0244

Gnomad4 FIN exome AF: 0.00529

Gnomad4 NFE exome AF: 0.0337

Gnomad4 OTH exome AF: 0.0340

GnomAD4 genome AF: 0.0205 AC: 3122 AN: 152266 Hom.: 51 Cov.: 33 AF XY: 0.0190 AC XY: 1414 AN XY: 74448

Gnomad4 AFR AF: 0.00529

Gnomad4 AMR AF: 0.0238

Gnomad4 ASJ AF: 0.0734

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.00283

Gnomad4 NFE AF: 0.0302

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0238 Hom.: 8

Bravo AF: 0.0221

Asia WGS AF: 0.0100 AC: 35 AN: 3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.10
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs146029473; hg19: chr7-36429300;