8-11319901-G-T

Variant names:

• chr8-11319901-G-T
• rs2293855
• ENST00000498997.3:n.1814C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000498997.3(ENSG00000246477):​n.1814C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,402,980 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ENSG00000246477 ENST00000498997.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 0 publications found

Genes affected

ENSG00000246477 (HGNC:58409):

MTMR9 (HGNC:14596): (myotubularin related protein 9) This gene encodes a myotubularin-related protein that is atypical to most other members of the myotubularin-related protein family because it has no dual-specificity phosphatase domain. The encoded protein contains a double-helical motif similar to the SET interaction domain, which is thought to have a role in the control of cell proliferation. In mouse, a protein similar to the encoded protein binds with MTMR7, and together they dephosphorylate phosphatidylinositol 3-phosphate and inositol 1,3-bisphosphate. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTMR9	NM_015458.4	c.1486+63G>T		intron_variant	Intron 9 of 9	ENST00000221086.8	NP_056273.2
MTMR9-AS1	NR_189628.1	n.1813C>A		non_coding_transcript_exon_variant	Exon 2 of 2
MTMR9	XM_047422125.1	c.1486+63G>T		intron_variant	Intron 9 of 10		XP_047278081.1
MTMR9	XM_011543831.3	c.898+63G>T		intron_variant	Intron 7 of 7		XP_011542133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246477	ENST00000498997.3	n.1814C>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
MTMR9	ENST00000221086.8	c.1486+63G>T		intron_variant	Intron 9 of 9	1	NM_015458.4	ENSP00000221086.3
MTMR9	ENST00000530200.1	n.*1232+63G>T		intron_variant	Intron 10 of 10	1		ENSP00000436046.1
MTMR9	ENST00000526292.1	c.1231+63G>T		intron_variant	Intron 9 of 9	2		ENSP00000433239.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000143 AC: 2 AN: 1402980 Hom.: 0 Cov.: 21 AF XY: 0.00000144 AC XY: 1 AN XY: 696774

African (AFR) AF: 0.00 AC: 0 AN: 32110

American (AMR) AF: 0.00 AC: 0 AN: 41664

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24246

East Asian (EAS) AF: 0.00 AC: 0 AN: 39196

South Asian (SAS) AF: 0.00 AC: 0 AN: 80648

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51806

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5566

European-Non Finnish (NFE) AF: 0.00000187 AC: 2 AN: 1069494

Other (OTH) AF: 0.00 AC: 0 AN: 58250

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.69
PhyloP100		-0.44

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: rs2293855; hg19: chr8-11177410;