3-9657375-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001077525.3(MTMR14):​c.308+3606G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,084 control chromosomes in the GnomAD database, including 4,977 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 0.19 ( 4977 hom., cov: 32)

Consequence

MTMR14
NM_001077525.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0100
Variant links:
Genes affected
MTMR14 (HGNC:26190): (myotubularin related protein 14) This gene encodes a myotubularin-related protein. The encoded protein is a phosphoinositide phosphatase that specifically dephosphorylates phosphatidylinositol 3,5-biphosphate and phosphatidylinositol 3-phosphate. Mutations in this gene are correlated with autosomal dominant centronuclear myopathy. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 18.[provided by RefSeq, Apr 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MTMR14NM_001077525.3 linkuse as main transcriptc.308+3606G>C intron_variant ENST00000296003.9 NP_001070993.1 Q8NCE2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MTMR14ENST00000296003.9 linkuse as main transcriptc.308+3606G>C intron_variant 1 NM_001077525.3 ENSP00000296003.5 Q8NCE2-1

Frequencies

GnomAD3 genomes
AF:
0.194
AC:
29538
AN:
151966
Hom.:
4947
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.460
Gnomad AMI
AF:
0.0241
Gnomad AMR
AF:
0.165
Gnomad ASJ
AF:
0.104
Gnomad EAS
AF:
0.0603
Gnomad SAS
AF:
0.0727
Gnomad FIN
AF:
0.0653
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.0865
Gnomad OTH
AF:
0.174
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.195
AC:
29614
AN:
152084
Hom.:
4977
Cov.:
32
AF XY:
0.192
AC XY:
14274
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.460
Gnomad4 AMR
AF:
0.165
Gnomad4 ASJ
AF:
0.104
Gnomad4 EAS
AF:
0.0600
Gnomad4 SAS
AF:
0.0736
Gnomad4 FIN
AF:
0.0653
Gnomad4 NFE
AF:
0.0865
Gnomad4 OTH
AF:
0.173
Alfa
AF:
0.0418
Hom.:
41
Bravo
AF:
0.216
Asia WGS
AF:
0.107
AC:
371
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.2
DANN
Benign
0.73

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3868891; hg19: chr3-9699059; API