chr6-150898848-T-TATTATG

Variant names:

• chr6-150898848-T-TATTATG
• rs3832406
• NM_015440.5:c.781-6802_781-6801insATTATG

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_015440.5(MTHFD1L):​c.781-6802_781-6801insATTATG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: MTHFD1L NM_015440.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• Publications: 7 publications found

Genes affected

MTHFD1L (HGNC:21055): (methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like) The protein encoded by this gene is involved in the synthesis of tetrahydrofolate (THF) in the mitochondrion. THF is important in the de novo synthesis of purines and thymidylate and in the regeneration of methionine from homocysteine. Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jun 2011]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015440.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTHFD1L	NM_015440.5	MANE Select	c.781-6802_781-6801insATTATG		intron	N/A	NP_056255.2
	MTHFD1L	NM_001242767.2		c.784-6802_784-6801insATTATG		intron	N/A	NP_001229696.1
	MTHFD1L	NM_001242768.2		c.586-6802_586-6801insATTATG		intron	N/A	NP_001229697.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTHFD1L	ENST00000367321.8	TSL:1 MANE Select	c.781-6802_781-6801insATTATG		intron	N/A	ENSP00000356290.3
	MTHFD1L	ENST00000367307.8	TSL:1	c.781-12_781-11insATTATG		intron	N/A	ENSP00000356276.4
	MTHFD1L	ENST00000611279.4	TSL:5	c.784-6802_784-6801insATTATG		intron	N/A	ENSP00000478253.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 1

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs3832406; hg19: chr6-151219984;