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GeneBe

1-11786602-ATTTT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_005957(MTHFR):c.*4074_*4077del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.54 ( 21344 hom., cov: 0)

Consequence

MTHFR
NM_005957 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.308

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
?
Variant 1:11786602-ATTTT>A is Benign according to our data. Variant chr1-11786602-ATTTT-A is described in ClinVar as [Likely_benign]. Clinvar id is 292164. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MTHFRNM_005957.5 linkuse as main transcriptc.*4074_*4077del 3_prime_UTR_variant 12/12 ENST00000376590.9
C1orf167NM_001010881.2 linkuse as main transcriptc.3568-770_3568-767del intron_variant ENST00000688073.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MTHFRENST00000376590.9 linkuse as main transcriptc.*4074_*4077del 3_prime_UTR_variant 12/121 NM_005957.5 A1P42898-1
C1orf167ENST00000688073.1 linkuse as main transcriptc.3568-770_3568-767del intron_variant NM_001010881.2 A2

Frequencies

GnomAD3 genomes
AF:
0.542
AC:
76895
AN:
141988
Hom.:
21344
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.387
Gnomad AMI
AF:
0.594
Gnomad AMR
AF:
0.689
Gnomad ASJ
AF:
0.626
Gnomad EAS
AF:
0.759
Gnomad SAS
AF:
0.454
Gnomad FIN
AF:
0.621
Gnomad MID
AF:
0.524
Gnomad NFE
AF:
0.575
Gnomad OTH
AF:
0.556
GnomAD4 exome
AF:
0.250
AC:
1
AN:
4
Hom.:
0
AC XY:
0
AN XY:
0
show subpopulations
Gnomad4 NFE exome
AF:
0.250

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Neural tube defects, folate-sensitive Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores 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: rs55780505; hg19: chr1-11846659;