chr5-94839676-T-C

Variant names:

• chr5-94839676-T-C
• rs255211
• NM_024717.7:c.2436+28657A>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.2436+28657A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 152,212 control chromosomes in the GnomAD database, including 60,968 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 0.89 (60968 hom., cov: 31)
• Consequence: MCTP1 NM_024717.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCTP1	NM_024717.7	c.2436+28657A>G		intron_variant	Intron 17 of 22	ENST00000515393.6	NP_078993.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCTP1	ENST00000515393.6	c.2436+28657A>G		intron_variant	Intron 17 of 22	1	NM_024717.7	ENSP00000424126.1

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135761 AN: 152094 Hom.: 60916 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.893 AC: 135864 AN: 152212 Hom.: 60968 Cov.: 31 AF XY: 0.887 AC XY: 66000 AN XY: 74410

African (AFR) AF: 0.975 AC: 40528 AN: 41558

American (AMR) AF: 0.810 AC: 12371 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3137 AN: 3470

East Asian (EAS) AF: 0.929 AC: 4806 AN: 5174

South Asian (SAS) AF: 0.793 AC: 3815 AN: 4810

European-Finnish (FIN) AF: 0.833 AC: 8826 AN: 10594

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59377 AN: 68016

Other (OTH) AF: 0.889 AC: 1874 AN: 2108

Alfa AF: 0.881 Hom.: 127124

Bravo AF: 0.897

Asia WGS AF: 0.845 AC: 2935 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		-0.99
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: rs255211; hg19: chr5-94175381;