1-167917264-A-T

Position:

• chr1-167917264-A-T

Variant summary

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

The NM_001143674.4(MPC2):​c.*1059T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,090 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)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: MPC2 NM_001143674.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

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:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MPC2	NM_001143674.4	c.*1059T>A		3_prime_UTR_variant	6/6	ENST00000271373.9	NP_001137146.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MPC2	ENST00000271373.9	c.*1059T>A		3_prime_UTR_variant	6/6	1	NM_001143674.4	ENSP00000271373	P1
MPC2	ENST00000367846.8	c.*1059T>A		3_prime_UTR_variant	5/5	1		ENSP00000356820	P1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30827 AN: 151960 Hom.: 3824 Cov.: 32

Gnomad AFR AF: 0.0811

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: 0.288

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.218

GnomAD4 exome AF: 0.333 AC: 4 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.203 AC: 30839 AN: 152078 Hom.: 3827 Cov.: 32 AF XY: 0.204 AC XY: 15173 AN XY: 74306

Gnomad4 AFR AF: 0.0809

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.218

Alfa AF: 0.222 Hom.: 560

Bravo AF: 0.213

Asia WGS AF: 0.158 AC: 552 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	3.7
DANN	Benign	0.43

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: rs2420; hg19: chr1-167886502;