chr4-74295107-C-T

Position:

• chr4-74295107-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144978.3(MTHFD2L):​c.932-6590C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 151,956 control chromosomes in the GnomAD database, including 2,860 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 0.12 (2860 hom., cov: 32)
• Consequence: MTHFD2L NM_001144978.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

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]

LOC105377276 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTHFD2L	NM_001144978.3	c.932-6590C>T		intron_variant		ENST00000325278.7
LOC105377276	XR_938877.3	n.273-16329G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTHFD2L	ENST00000325278.7	c.932-6590C>T		intron_variant		5	NM_001144978.3	P1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17948 AN: 151838 Hom.: 2844 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.0534

Gnomad SAS AF: 0.0790

Gnomad FIN AF: 0.00896

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.119 AC: 18020 AN: 151956 Hom.: 2860 Cov.: 32 AF XY: 0.117 AC XY: 8716 AN XY: 74278

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.0750

Gnomad4 ASJ AF: 0.00375

Gnomad4 EAS AF: 0.0537

Gnomad4 SAS AF: 0.0797

Gnomad4 FIN AF: 0.00896

Gnomad4 NFE AF: 0.0130

Gnomad4 OTH AF: 0.0966

Alfa AF: 0.0273 Hom.: 449

Bravo AF: 0.134

Asia WGS AF: 0.103 AC: 357 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.46

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

Publications

LitVar

Other links and lift over

dbSNP: rs16850864; hg19: chr4-75160824;