1-11786035-G-GT

• Frequency: Genomes: 𝑓 0.98 (72488 hom., cov: 0)
• Consequence: MTHFR NM_005957 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.535

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1:11786035-G>GT is Benign according to our data. Variant chr1-11786035-G-GT is described in ClinVar as [Benign]. Clinvar id is 292153. Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTHFR	NM_005957.5	c.*4644_*4645insA		3_prime_UTR_variant	12/12	ENST00000376590.9
C1orf167	NM_001010881.2	c.3567+757dup		intron_variant		ENST00000688073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTHFR	ENST00000376590.9	c.*4644_*4645insA		3_prime_UTR_variant	12/12	1	NM_005957.5	A1
C1orf167	ENST00000688073.1	c.3567+757dup		intron_variant			NM_001010881.2	A2

Frequencies

GnomAD3 genomes AF: 0.984 AC: 147309 AN: 149702 Hom.: 72488 Cov.: 0

Gnomad AFR AF: 0.962

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.994

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.999

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.986

Alfa AF: 0.993 Hom.: 2192

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK:

Submissions by phenotype

Neural tube defects, folate-sensitive Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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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

Other links and lift over

dbSNP: rs55740775; hg19: chr1-11846092;