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

MTHFR (HGNC:7436):

C1orf167 (HGNC:25262):

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
MTHFR	NM_005957.5 linkuse as main transcript	c.4074_4077del		3_prime_UTR_variant	12/12	ENST00000376590.9
C1orf167	NM_001010881.2 linkuse as main transcript	c.3568-770_3568-767del		intron_variant		ENST00000688073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTHFR	ENST00000376590.9 linkuse as main transcript	c.4074_4077del		3_prime_UTR_variant	12/12	1	NM_005957.5	A1	P42898-1
C1orf167	ENST00000688073.1 linkuse as main transcript	c.3568-770_3568-767del		intron_variant			NM_001010881.2	A2

Frequencies

GnomAD3 genomes

AF:

0.542

AC:

76895

AN:

141988

Hom.:

21344

Cov.:

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:

AN:

Hom.:

AC XY:

AN XY:

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 submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 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.