16-83907796-A-G

Position:

• chr16-83907796-A-G

Variant summary

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

The NM_012213.3(MLYCD):​c.642-330A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,062 control chromosomes in the GnomAD database, including 4,747 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 0.23 (4747 hom., cov: 32)
• Consequence: MLYCD NM_012213.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

MLYCD (HGNC:7150): (malonyl-CoA decarboxylase) The product of this gene catalyzes the breakdown of malonyl-CoA to acetyl-CoA and carbon dioxide. Malonyl-CoA is an intermediate in fatty acid biosynthesis, and also inhibits the transport of fatty acyl CoAs into mitochondria. Consequently, the encoded protein acts to increase the rate of fatty acid oxidation. It is found in mitochondria, peroxisomes, and the cytoplasm. Mutations in this gene result in malonyl-CoA decarboyxlase deficiency. [provided by RefSeq, Jul 2008]

ENSG00000288849 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLYCD	NM_012213.3	c.642-330A>G		intron_variant		ENST00000262430.6	NP_036345.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLYCD	ENST00000262430.6	c.642-330A>G		intron_variant		1	NM_012213.3	ENSP00000262430.4
ENSG00000288849	ENST00000689373.1	n.1315-330A>G		intron_variant
ENSG00000288849	ENST00000692462.1	n.1283-330A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34505 AN: 151944 Hom.: 4722 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.227 AC: 34586 AN: 152062 Hom.: 4747 Cov.: 32 AF XY: 0.224 AC XY: 16669 AN XY: 74330

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.193

Alfa AF: 0.165 Hom.: 3637

Bravo AF: 0.242

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.11
DANN	Benign	0.20

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: rs11649200; hg19: chr16-83941401;