rs469339

Variant names:

• chr5-94812833-G-A
• rs469339
• NM_024717.7:c.2437-13701C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-94812833-G-A
• chr5-94812833-G-C
• chr5-94812833-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024717.7(MCTP1):​c.2437-13701C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 151,518 control chromosomes in the GnomAD database, including 70,318 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 0.96 (70318 hom., cov: 27)
• Consequence: MCTP1 NM_024717.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCTP1	NM_024717.7	c.2437-13701C>T		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.2437-13701C>T		intron_variant	Intron 17 of 22	1	NM_024717.7	ENSP00000424126.1

Frequencies

GnomAD3 genomes AF: 0.962 AC: 145685 AN: 151400 Hom.: 70255 Cov.: 27

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.969

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.962 AC: 145809 AN: 151518 Hom.: 70318 Cov.: 27 AF XY: 0.958 AC XY: 70849 AN XY: 73970

African (AFR) AF: 0.993 AC: 41010 AN: 41306

American (AMR) AF: 0.965 AC: 14676 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 3394 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3872 AN: 5142

South Asian (SAS) AF: 0.870 AC: 4182 AN: 4806

European-Finnish (FIN) AF: 0.934 AC: 9637 AN: 10318

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.969 AC: 65877 AN: 67968

Other (OTH) AF: 0.965 AC: 2024 AN: 2098

Alfa AF: 0.975 Hom.: 32130

Bravo AF: 0.969

Asia WGS AF: 0.815 AC: 2836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.0
DANN	Benign	0.49
PhyloP100		0.13
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: rs469339; hg19: chr5-94148538;