rs153291

Positions:

• chr5-95254001-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.720+29855A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,880 control chromosomes in the GnomAD database, including 10,785 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 0.38 (10785 hom., cov: 32)
• Consequence: MCTP1 NM_024717.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

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]

LOC105379085 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MCTP1	NM_024717.7	c.720+29855A>G		intron_variant		ENST00000515393.6
LOC105379085	XR_948575.3	n.914-1703T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCTP1	ENST00000515393.6	c.720+29855A>G		intron_variant		1	NM_024717.7	P2
MCTP1	ENST00000503301.5	c.145+29855A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56967 AN: 151762 Hom.: 10744 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.376 AC: 57071 AN: 151880 Hom.: 10785 Cov.: 32 AF XY: 0.374 AC XY: 27759 AN XY: 74232

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.380

Alfa AF: 0.394 Hom.: 1673

Bravo AF: 0.369

Asia WGS AF: 0.340 AC: 1188 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.5
DANN	Benign	0.79

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: rs153291; hg19: chr5-94589705;