ENST00000429335.5:n.-107+4970C>T

Variant names:

• chr4-74128207-T-.
• ENST00000429335.5:n.-107+2690T>.

Variant summary

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

The ENST00000429335.5(MTHFD2L):​n.-107+2690T>. variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 N/A (N/A hom., cov:)
  • Exomes 𝑓: N/A (N/A hom.)
• Consequence: MTHFD2L ENST00000429335.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

MTHFD2L (HGNC:31865): (methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2 like) Predicted to enable methenyltetrahydrofolate cyclohydrolase activity; methylenetetrahydrofolate dehydrogenase (NAD+) activity; and methylenetetrahydrofolate dehydrogenase (NADP+) activity. Predicted to be involved in tetrahydrofolate interconversion. Predicted to be located in mitochondrial matrix. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

LOC105377277 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTHFD2L	NM_001351310.2	c.-66+2690T>.		intron_variant	Intron 2 of 8		NP_001338239.1
MTHFD2L	NM_001351311.2	c.-32+2690T>.		intron_variant	Intron 2 of 7		NP_001338240.1
MTHFD2L	XM_017008218.3	c.-3831+2690T>.		intron_variant	Intron 3 of 12		XP_016863707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTHFD2L	ENST00000429335.5	n.-107+2690T>.		intron_variant	Intron 2 of 6	1		ENSP00000409391.1
MTHFD2L	ENST00000433372.5	n.80+2690T>.		intron_variant	Intron 1 of 7	1
MTHFD2L	ENST00000429519.5	n.458+2690T>.		intron_variant	Intron 3 of 9	5

Frequencies

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

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-74993924;