rs162033

chr5-7880722-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002454.3(MTRR):c.780+2400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,978 control chromosomes in the GnomAD database, including 17,528 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (17528 hom., cov: 32)
• Consequence: MTRR NM_002454.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

MTRR (HGNC:7473): (5-methyltetrahydrofolate-homocysteine methyltransferase reductase) This gene encodes a member of the ferredoxin-NADP(+) reductase (FNR) family of electron transferases. This protein functions in the synthesis of methionine by regenerating methionine synthase to a functional state. Because methionine synthesis requires methyl-group transfer by a folate donor, activity of the encoded enzyme is important for folate metabolism and cellular methylation. Mutations in this gene can cause homocystinuria-megaloblastic anemia, cbl E type. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTRR	NM_002454.3	c.780+2400C>T		intron_variant		ENST00000440940.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTRR	ENST00000440940.7	c.780+2400C>T		intron_variant		1	NM_002454.3	P1

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71224 AN: 151862 Hom.: 17506 Cov.: 32

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.448

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.469 AC: 71287 AN: 151978 Hom.: 17528 Cov.: 32 AF XY: 0.467 AC XY: 34714 AN XY: 74270

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.446

Alfa AF: 0.432 Hom.: 5133

Bravo AF: 0.483

Asia WGS AF: 0.330 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.44
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs162033; hg19: chr5-7880835;