1-11786602-A-ATT

• Frequency: Genomes: 𝑓 0.12 (1244 hom., cov: 0)
• Consequence: MTHFR NM_005957 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTHFR	NM_005957.5	c.*4077_*4078insAA		3_prime_UTR_variant	12/12	ENST00000376590.9
C1orf167	NM_001010881.2	c.3568-768_3568-767dup		intron_variant		ENST00000688073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTHFR	ENST00000376590.9	c.*4077_*4078insAA		3_prime_UTR_variant	12/12	1	NM_005957.5	A1
C1orf167	ENST00000688073.1	c.3568-768_3568-767dup		intron_variant			NM_001010881.2	A2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 16356 AN: 141838 Hom.: 1244 Cov.: 0

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.250

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK:

Submissions by phenotype

Neural tube defects, folate-sensitive Uncertain:1

Uncertain significance, 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 SpliceAI and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs55780505; hg19: chr1-11846659;