1-11790698-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM2_SupportingBP4_ModerateBP6_ModerateBP7

The NM_005957(MTHFR):c.1953A>G(p.Arg651=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 33)

Consequence

MTHFR
NM_005957 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.891

Links

MTHFR (HGNC:7436):

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2

Very rare variant; Number of alleles below threshold, Median coverage is 33.

BP4

Computational evidence support a benign effect (MetaRNN=0.086651295).

BP6

Variant 1:11790698-T>C is Benign according to our data. Variant chr1-11790698-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1596851. Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.891 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTHFR	NM_005957.5 linkuse as main transcript	c.1953A>G	p.Arg651=	synonymous_variant	12/12	ENST00000376590.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTHFR	ENST00000376590.9 linkuse as main transcript	c.1953A>G	p.Arg651=	synonymous_variant	12/12	1	NM_005957.5	A1	P42898-1

Frequencies

GnomAD3 genomes

Cov.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Homocystinuria due to methylene tetrahydrofolate reductase deficiency

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Nov 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

Cadd

Benign

0.52

Dann

Benign

0.57

FATHMM_MKL

Benign

0.026

LIST_S2

Benign

0.29

MetaRNN

Benign

0.087

MutationTaster

Benign

1.0

N;N;N;N

GERP RS

-6.7

Splicing

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

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over