15-30971069-C-T

Variant names:

• chr15-30971069-C-T
• rs1524876
• NM_017762.3:c.475-3059G>A

Variant summary

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

The NM_017762.3(MTMR10):​c.475-3059G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,838 control chromosomes in the GnomAD database, including 14,378 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 0.41 (14378 hom., cov: 31)
• Consequence: MTMR10 NM_017762.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 10 publications found

Genes affected

MTMR10 (HGNC:25999): (myotubularin related protein 10) Predicted to enable phosphatidylinositol-3-phosphatase activity. Predicted to be involved in phosphatidylinositol dephosphorylation. Located in cytoplasm. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017762.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTMR10	NM_017762.3	MANE Select	c.475-3059G>A		intron	N/A	NP_060232.2	X5D963

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTMR10	ENST00000435680.6	TSL:1 MANE Select	c.475-3059G>A		intron	N/A	ENSP00000402537.1	Q9NXD2-1
	MTMR10	ENST00000568604.5	TSL:1	n.474+3245G>A		intron	N/A	ENSP00000457903.1	Q9NXD2-3
	MTMR10	ENST00000879100.1		c.472-3059G>A		intron	N/A	ENSP00000549159.1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62724 AN: 151718 Hom.: 14365 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.413 AC: 62744 AN: 151838 Hom.: 14378 Cov.: 31 AF XY: 0.424 AC XY: 31436 AN XY: 74198

African (AFR) AF: 0.231 AC: 9579 AN: 41412

American (AMR) AF: 0.508 AC: 7753 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1827 AN: 3468

East Asian (EAS) AF: 0.851 AC: 4390 AN: 5156

South Asian (SAS) AF: 0.543 AC: 2611 AN: 4808

European-Finnish (FIN) AF: 0.474 AC: 4992 AN: 10542

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30161 AN: 67890

Other (OTH) AF: 0.413 AC: 869 AN: 2106

Alfa AF: 0.442 Hom.: 7221

Bravo AF: 0.410

Asia WGS AF: 0.637 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.39
PhyloP100		-0.50
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: rs1524876; hg19: chr15-31263272;