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GeneBe

1-11786618-TTTTG-T

Variant summary

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

The NM_005957(MTHFR):c.*4058_*4061del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 30)
Failed GnomAD Quality Control

Consequence

MTHFR
NM_005957 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.748

Links

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MTHFRNM_005957.5 linkuse as main transcriptc.*4058_*4061del 3_prime_UTR_variant 12/12 ENST00000376590.9
C1orf167NM_001010881.2 linkuse as main transcriptc.3568-768_3568-765del intron_variant ENST00000688073.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MTHFRENST00000376590.9 linkuse as main transcriptc.*4058_*4061del 3_prime_UTR_variant 12/121 NM_005957.5 A1P42898-1
C1orf167ENST00000688073.1 linkuse as main transcriptc.3568-768_3568-765del intron_variant NM_001010881.2 A2

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
10
AN:
111598
Hom.:
0
Cov.:
30
FAILED QC
Gnomad AFR
AF:
0.0000956
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000197
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000146
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000780
Gnomad OTH
AF:
0.00
Alfa
AF:
0.000307
Hom.:
0

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Neural tube defects, folate-sensitive Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs886045172; hg19: chr1-11846675;