rs7176028

Positions:

• chr15-94418016-A-G

Variant summary

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

The NM_001385001.1(MCTP2):​c.2085+15997A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,148 control chromosomes in the GnomAD database, including 1,948 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 0.16 (1948 hom., cov: 32)
• Consequence: MCTP2 NM_001385001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525

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]

MCTP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MCTP2	NM_001385001.1	c.2085+15997A>G		intron_variant		ENST00000357742.10	NP_001371930.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MCTP2	ENST00000357742.10	c.2085+15997A>G		intron_variant		1	NM_001385001.1	ENSP00000350377.4
MCTP2	ENST00000451018.7	c.2085+15997A>G		intron_variant		1		ENSP00000395109.3
MCTP2	ENST00000456504.5	n.*1623+15997A>G		intron_variant		1		ENSP00000388887.1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23951 AN: 152030 Hom.: 1948 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.157 AC: 23948 AN: 152148 Hom.: 1948 Cov.: 32 AF XY: 0.162 AC XY: 12032 AN XY: 74386

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.170

Alfa AF: 0.150 Hom.: 2546

Bravo AF: 0.155

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	9.8
DANN	Benign	0.59

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: rs7176028; hg19: chr15-94961245;