rs10489202

Variant names:

• chr1-167933841-G-T
• rs10489202
• NM_001143674.4:c.109+1892C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001143674.4(MPC2):​c.109+1892C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,140 control chromosomes in the GnomAD database, including 3,827 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 0.20 (3827 hom., cov: 32)
• Consequence: MPC2 NM_001143674.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684
• Publications: 48 publications found

Genes affected

MPC2 (HGNC:24515): (mitochondrial pyruvate carrier 2) Enables identical protein binding activity. Predicted to be involved in mitochondrial pyruvate transmembrane transport. Predicted to act upstream of or within mitochondrial acetyl-CoA biosynthetic process from pyruvate and positive regulation of insulin secretion involved in cellular response to glucose stimulus. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

DCAF6 (HGNC:30002): (DDB1 and CUL4 associated factor 6) The protein encoded by this gene is a ligand-dependent coactivator of nuclear receptors, including nuclear receptor subfamily 3 group C member 1 (NR3C1), glucocorticoid receptor (GR), and androgen receptor (AR). The encoded protein and DNA damage binding protein 2 (DDB2) may act as tumor promoters and tumor suppressors, respectively, by regulating the level of androgen receptor in prostate tissues. In addition, this protein can act with glucocorticoid receptor to promote human papillomavirus gene expression. [provided by RefSeq, Mar 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPC2	NM_001143674.4	c.109+1892C>A		intron_variant	Intron 2 of 5	ENST00000271373.9	NP_001137146.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPC2	ENST00000271373.9	c.109+1892C>A		intron_variant	Intron 2 of 5	1	NM_001143674.4	ENSP00000271373.4
MPC2	ENST00000367846.8	c.109+1892C>A		intron_variant	Intron 1 of 4	1		ENSP00000356820.4
MPC2	ENST00000458574.1	c.109+1892C>A		intron_variant	Intron 2 of 4	5		ENSP00000392874.1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30844 AN: 152022 Hom.: 3824 Cov.: 32

Gnomad AFR AF: 0.0813

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.203 AC: 30855 AN: 152140 Hom.: 3827 Cov.: 32 AF XY: 0.204 AC XY: 15191 AN XY: 74372

African (AFR) AF: 0.0811 AC: 3367 AN: 41518

American (AMR) AF: 0.364 AC: 5559 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3472

East Asian (EAS) AF: 0.136 AC: 703 AN: 5180

South Asian (SAS) AF: 0.186 AC: 899 AN: 4830

European-Finnish (FIN) AF: 0.209 AC: 2205 AN: 10560

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16452 AN: 67986

Other (OTH) AF: 0.218 AC: 461 AN: 2110

Alfa AF: 0.233 Hom.: 18335

Bravo AF: 0.213

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.75
PhyloP100		0.68
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10489202; hg19: chr1-167903079;