rs17418283

chr5-94818883-T-C

Variant summary

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

The NM_024717.7(MCTP1):c.2437-19751A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,142 control chromosomes in the GnomAD database, including 4,043 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 0.20 (4043 hom., cov: 31)
• Consequence: MCTP1 NM_024717.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

MCTP1 (HGNC:26183): (multiple C2 and transmembrane domain containing 1) Enables calcium ion binding activity. Predicted to be involved in several processes, including modulation of chemical synaptic transmission; negative regulation of endocytosis; and negative regulation of response to oxidative stress. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MCTP1	NM_024717.7	c.2437-19751A>G		intron_variant		ENST00000515393.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCTP1	ENST00000515393.6	c.2437-19751A>G		intron_variant		1	NM_024717.7	P2

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30578 AN: 152024 Hom.: 4041 Cov.: 31

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.201 AC: 30581 AN: 152142 Hom.: 4043 Cov.: 31 AF XY: 0.194 AC XY: 14426 AN XY: 74382

Gnomad4 AFR AF: 0.0533

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.0605

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.252

Alfa AF: 0.285 Hom.: 11313

Bravo AF: 0.195

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.8
Dann	Benign	0.75

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: rs17418283; hg19: chr5-94154588;