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GeneBe

1-11790681-C-T

Variant summary

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

The NM_005957(MTHFR):c.1970G>A(p.Ter657=) variant causes a stop retained 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 stop_retained

Scores

6

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.559

Links

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=0.10742256).
BP6
?
Variant 1:11790681-C>T is Benign according to our data. Variant chr1-11790681-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1540182. Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.559 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MTHFRNM_005957.5 linkuse as main transcriptc.1970G>A p.Ter657= stop_retained_variant 12/12 ENST00000376590.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MTHFRENST00000376590.9 linkuse as main transcriptc.1970G>A p.Ter657= stop_retained_variant 12/121 NM_005957.5 A1P42898-1

Frequencies

GnomAD3 genomes
Cov.:
33

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 submitterclinical testingInvitaeAug 28, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
Cadd
Benign
5.5
Dann
Benign
0.71
FATHMM_MKL
Benign
0.041
N
LIST_S2
Benign
0.26
T
MetaRNN
Benign
0.11
T
MutationTaster
Benign
1.0
N;N;N;N
GERP RS
3.0

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: chr1-11850738;