rs3784639

chr15-94473640-T-C

Variant summary

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

The NM_001385001.1(MCTP2):c.2471-3056T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,304 control chromosomes in the GnomAD database, including 221 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 0.039 (221 hom., cov: 33)
• Consequence: MCTP2 NM_001385001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

Genes affected

MCTP2 (HGNC:25636): (multiple C2 and transmembrane domain containing 2) Enables calcium ion binding activity. Predicted to be involved in regulation of neurotransmitter secretion. Located in cytosol and nucleoplasm. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MCTP2	NM_001385001.1	c.2471-3056T>C		intron_variant		ENST00000357742.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCTP2	ENST00000357742.10	c.2471-3056T>C		intron_variant		1	NM_001385001.1	P1
MCTP2	ENST00000451018.7	c.2306-3056T>C		intron_variant		1
MCTP2	ENST00000456504.5	c.*2009-3056T>C		intron_variant, NMD_transcript_variant		1
	ENST00000658115.1	n.170-15855A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0385 AC: 5860 AN: 152186 Hom.: 219 Cov.: 33

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0713

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00935

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0385 AC: 5868 AN: 152304 Hom.: 221 Cov.: 33 AF XY: 0.0418 AC XY: 3116 AN XY: 74472

Gnomad4 AFR AF: 0.0741

Gnomad4 AMR AF: 0.0198

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0719

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0574

Gnomad4 NFE AF: 0.00936

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0164 Hom.: 46

Bravo AF: 0.0358

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.9
Dann	Benign	0.83

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: rs3784639; hg19: chr15-95016869;