NM_000254.3:c.*1254A>C

Variant names:

• chr1-236898898-A-C
• rs2853523
• NM_000254.3:c.*1254A>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000254.3(MTR):​c.*1254A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,072 control chromosomes in the GnomAD database, including 40,642 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.72 (40641 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: MTR NM_000254.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.228
• Publications: 23 publications found

Genes affected

MTR (HGNC:7468): (5-methyltetrahydrofolate-homocysteine methyltransferase) This gene encodes the 5-methyltetrahydrofolate-homocysteine methyltransferase. This enzyme, also known as cobalamin-dependent methionine synthase, catalyzes the final step in methionine biosynthesis. Mutations in MTR have been identified as the underlying cause of methylcobalamin deficiency complementation group G. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]

MTR Gene-Disease associations (from GenCC):

• methylcobalamin deficiency type cblG

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), ClinGen, G2P

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 1-236898898-A-C is Benign according to our data. Variant chr1-236898898-A-C is described in ClinVar as Benign. ClinVar VariationId is 296610.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000254.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTR	NM_000254.3	MANE Select	c.*1254A>C		3_prime_UTR	Exon 33 of 33	NP_000245.2	Q99707-1
	MTR	NM_001291939.1		c.*1254A>C		3_prime_UTR	Exon 32 of 32	NP_001278868.1	Q99707-2
	MTR	NM_001410942.1		c.*1254A>C		3_prime_UTR	Exon 31 of 31	NP_001397871.1	A0A7P0TAJ0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTR	ENST00000366577.10	TSL:1 MANE Select	c.*1254A>C		3_prime_UTR	Exon 33 of 33	ENSP00000355536.5	Q99707-1
	MTR	ENST00000366576.3	TSL:1	c.*1254A>C		3_prime_UTR	Exon 20 of 20	ENSP00000355535.3	B1ANE3
	MTR	ENST00000961801.1		c.*1254A>C		3_prime_UTR	Exon 31 of 31	ENSP00000631860.1

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109281 AN: 151950 Hom.: 40590 Cov.: 32

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.622

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.675

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.719 AC: 109396 AN: 152068 Hom.: 40641 Cov.: 32 AF XY: 0.720 AC XY: 53530 AN XY: 74300

African (AFR) AF: 0.911 AC: 37811 AN: 41510

American (AMR) AF: 0.670 AC: 10231 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1852 AN: 3468

East Asian (EAS) AF: 0.813 AC: 4199 AN: 5166

South Asian (SAS) AF: 0.727 AC: 3504 AN: 4820

European-Finnish (FIN) AF: 0.651 AC: 6865 AN: 10546

Middle Eastern (MID) AF: 0.631 AC: 183 AN: 290

European-Non Finnish (NFE) AF: 0.627 AC: 42589 AN: 67968

Other (OTH) AF: 0.679 AC: 1432 AN: 2110

Alfa AF: 0.650 Hom.: 43035

Bravo AF: 0.730

Asia WGS AF: 0.771 AC: 2678 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	Disorders of Intracellular Cobalamin Metabolism (1)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.85
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2853523; hg19: chr1-237062198;