6-49431526-A-AT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000255.4(MMUT):c.*201_*202insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.020 (82 hom., cov: 0)
  • Exomes 𝑓: 0.0051 (9 hom.)
• Consequence: MMUT NM_000255.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0410

Genes affected

MMUT (HGNC:7526): (methylmalonyl-CoA mutase) This gene encodes the mitochondrial enzyme methylmalonyl Coenzyme A mutase. In humans, the product of this gene is a vitamin B12-dependent enzyme which catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA, while in other species this enzyme may have different functions. Mutations in this gene may lead to various types of methylmalonic aciduria. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-49431526-A-AT is Benign according to our data. Variant chr6-49431526-A-AT is described in ClinVar as [Benign]. Clinvar id is 1227019.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMUT	NM_000255.4	c.*201_*202insA		3_prime_UTR_variant	13/13	ENST00000274813.4
MMUT	XM_005249143.4	c.*201_*202insA		3_prime_UTR_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMUT	ENST00000274813.4	c.*201_*202insA		3_prime_UTR_variant	13/13	1	NM_000255.4	P1

Frequencies

GnomAD3 genomes AF: 0.0201 AC: 3020 AN: 150536 Hom.: 82 Cov.: 0

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00937

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.000390

Gnomad SAS AF: 0.00105

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00962

Gnomad NFE AF: 0.00182

Gnomad OTH AF: 0.0126

GnomAD4 exome AF: 0.00510 AC: 1571 AN: 307790 Hom.: 9 Cov.: 0 AF XY: 0.00471 AC XY: 771 AN XY: 163780

Gnomad4 AFR exome AF: 0.0660

Gnomad4 AMR exome AF: 0.00864

Gnomad4 ASJ exome AF: 0.00732

Gnomad4 EAS exome AF: 0.00238

Gnomad4 SAS exome AF: 0.00148

Gnomad4 FIN exome AF: 0.00139

Gnomad4 NFE exome AF: 0.00289

Gnomad4 OTH exome AF: 0.00853

GnomAD4 genome AF: 0.0201 AC: 3024 AN: 150646 Hom.: 82 Cov.: 0 AF XY: 0.0191 AC XY: 1402 AN XY: 73518

Gnomad4 AFR AF: 0.0660

Gnomad4 AMR AF: 0.00936

Gnomad4 ASJ AF: 0.00375

Gnomad4 EAS AF: 0.000392

Gnomad4 SAS AF: 0.000842

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00181

Gnomad4 OTH AF: 0.0125

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 05, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs10713340; hg19: chr6-49399239;