Variant rs71391718 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000624835.2(ENSG00000279070):n.230_254delinsCAACACAAGAGAAA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Consequence

ENST00000624835.2 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.550

Variant links:

Genes affected

(HGNC:):

links:

MTHFD2 (HGNC:7434): (methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase) This gene encodes a nuclear-encoded mitochondrial bifunctional enzyme with methylenetetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclohydrolase activities. The enzyme functions as a homodimer and is unique in its absolute requirement for magnesium and inorganic phosphate. Formation of the enzyme-magnesium complex allows binding of NAD. Alternative splicing results in two different transcripts, one protein-coding and the other not protein-coding. This gene has a pseudogene on chromosome 7. [provided by RefSeq, Mar 2009]

MTHFD2 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	Protein	UniProt
	ENST00000624835.2 linkuse as main transcript	n.230_254delinsCAACACAAGAGAAA	non_coding_transcript_exon_variant	1/1
MTHFD2	ENST00000677170.1 linkuse as main transcript	c.-303-3075_-303-3051delinsTTTCTCTTGTGTTG	intron_variant		ENSP00000503486	P13995-2
MTHFD2	ENST00000677997.1 linkuse as main transcript	c.24-7398_24-7374delinsTTTCTCTTGTGTTG	intron_variant		ENSP00000503074
MTHFD2	ENST00000678684.1 linkuse as main transcript	c.-205-7398_-205-7374delinsTTTCTCTTGTGTTG	intron_variant		ENSP00000504687	P13995-2

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.