rs17339892

chr5-95049359-G-Achr5-95049359-G-T

Variant summary

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

The NM_024717.7(MCTP1):c.721-31875C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,022 control chromosomes in the GnomAD database, including 4,044 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 0.21 (4044 hom., cov: 32)
• Consequence: MCTP1 NM_024717.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) 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.721-31875C>T		intron_variant		ENST00000515393.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCTP1	ENST00000515393.6	c.721-31875C>T		intron_variant		1	NM_024717.7	P2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31837 AN: 151902 Hom.: 4040 Cov.: 32

Gnomad AFR AF: 0.0677

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.209 AC: 31841 AN: 152022 Hom.: 4044 Cov.: 32 AF XY: 0.204 AC XY: 15175 AN XY: 74294

Gnomad4 AFR AF: 0.0675

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.227

Alfa AF: 0.253 Hom.: 2780

Bravo AF: 0.211

Asia WGS AF: 0.133 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.0
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: rs17339892; hg19: chr5-94385063;