4-145619443-G-C

Variant names:

• chr4-145619443-G-C
• rs140592995
• NM_172250.3:c.-66+36G>C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001375644.1(MMAA):​c.-272G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00732 in 152,336 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0073 (12 hom., cov: 32)
  • Exomes 𝑓: 0.027 (0 hom.)
• Consequence: MMAA NM_001375644.1 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.60

Genes affected

MMAA (HGNC:18871): (metabolism of cobalamin associated A) The protein encoded by this gene is involved in the translocation of cobalamin into the mitochondrion, where it is used in the final steps of adenosylcobalamin synthesis. Adenosylcobalamin is a coenzyme required for the activity of methylmalonyl-CoA mutase. Defects in this gene are a cause of methylmalonic aciduria. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 4-145619443-G-C is Benign according to our data. Variant chr4-145619443-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1326747.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency = 0.0714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMAA	NM_172250.3	c.-66+36G>C		intron_variant	Intron 1 of 6	ENST00000649156.2	NP_758454.1
MMAA	NM_001375644.1	c.-272G>C		5_prime_UTR_variant	Exon 1 of 7		NP_001362573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMAA	ENST00000649156.2	c.-66+36G>C		intron_variant	Intron 1 of 6		NM_172250.3	ENSP00000497008.1

Frequencies

GnomAD3 genomes AF: 0.00732 AC: 1113 AN: 152144 Hom.: 12 Cov.: 32

Gnomad AFR AF: 0.00200

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00589

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00786

Gnomad FIN AF: 0.0146

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.00716

GnomAD4 exome AF: 0.0270 AC: 2 AN: 74 Hom.: 0 Cov.: 0 AF XY: 0.0200 AC XY: 1 AN XY: 50

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 0.0714

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0185

GnomAD4 genome AF: 0.00731 AC: 1113 AN: 152262 Hom.: 12 Cov.: 32 AF XY: 0.00721 AC XY: 537 AN XY: 74464

Gnomad4 AFR AF: 0.00200

Gnomad4 AMR AF: 0.00588

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00787

Gnomad4 FIN AF: 0.0146

Gnomad4 NFE AF: 0.0103

Gnomad4 OTH AF: 0.00709

Alfa AF: 0.00725 Hom.: 1

Bravo AF: 0.00671

Asia WGS AF: 0.00491 AC: 17 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 24, 2021

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.024
DANN	Benign	0.44

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: rs140592995; hg19: chr4-146540595;