rs153291

Variant names:

• chr5-95254001-T-C
• rs153291
• NM_024717.7:c.720+29855A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MCTP1	NM_024717.7	c.720+29855A>G		intron_variant	Intron 1 of 22	ENST00000515393.6	NP_078993.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCTP1	ENST00000515393.6	c.720+29855A>G		intron_variant	Intron 1 of 22	1	NM_024717.7	ENSP00000424126.1
MCTP1	ENST00000503301.5	c.144+29855A>G		intron_variant	Intron 1 of 7	5		ENSP00000425515.1

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

African (AFR) AF: 0.406 AC: 16804 AN: 41430

American (AMR) AF: 0.308 AC: 4692 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1552 AN: 3464

East Asian (EAS) AF: 0.228 AC: 1178 AN: 5166

South Asian (SAS) AF: 0.366 AC: 1768 AN: 4826

European-Finnish (FIN) AF: 0.383 AC: 4039 AN: 10552

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25836 AN: 67886

Other (OTH) AF: 0.380 AC: 800 AN: 2108

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
PhyloP100		0.0080
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs153291; hg19: chr5-94589705;