Variant chr6-166365191-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_016098.4(MPC1):c.*238A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 374,584 control chromosomes in the GnomAD database, including 35,429 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.37 ( 12119 hom., cov: 33)

Exomes 𝑓: 0.45 ( 23310 hom. )

Consequence

MPC1
NM_016098.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.11

Variant links:

Genes affected

MPC1 (HGNC:21606): (mitochondrial pyruvate carrier 1) The protein encoded by this gene is part of an MPC1/MPC2 heterodimer that is responsible for transporting pyruvate into mitochondria. The encoded protein is found in the inner mitochondrial membrane. Defects in this gene are a cause of mitochondrial pyruvate carrier deficiency. Several transcript variants, some protein coding and one non-protein coding, have been found for this gene. [provided by RefSeq, Aug 2012]

MPC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 6-166365191-T-G is Benign according to our data. Variant chr6-166365191-T-G is described in ClinVar as [Benign]. Clinvar id is 1221336.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MPC1	NM_016098.4 linkuse as main transcript	c.*238A>C		3_prime_UTR_variant	5/5	ENST00000360961.11	NP_057182.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
MPC1	ENST00000360961.11 linkuse as main transcript	c.*238A>C	3_prime_UTR_variant	5/5	5	NM_016098.4	ENSP00000354223	P3
MPC1	ENST00000621630.1 linkuse as main transcript	c.*238A>C	3_prime_UTR_variant	5/5	5		ENSP00000479789	A1
MPC1	ENST00000487218.5 linkuse as main transcript	n.801A>C	non_coding_transcript_exon_variant	6/6	5
MPC1	ENST00000366868.5 linkuse as main transcript		downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

56142

AN:

151986

Hom.:

12109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.407

Gnomad AMR

AF:

0.425

Gnomad ASJ

AF:

0.400

Gnomad EAS

AF:

0.609

Gnomad SAS

AF:

0.669

Gnomad FIN

AF:

0.480

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.434

Gnomad OTH

AF:

0.369

GnomAD4 exome

AF:

0.450

AC:

100207

AN:

222480

Hom.:

23310

Cov.:

AF XY:

0.451

AC XY:

51460

AN XY:

114038

show subpopulations

Gnomad4 AFR exome

AF:

0.138

Gnomad4 AMR exome

AF:

0.471

Gnomad4 ASJ exome

AF:

0.409

Gnomad4 EAS exome

AF:

0.559

Gnomad4 SAS exome

AF:

0.702

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.440

Gnomad4 OTH exome

AF:

0.428

GnomAD4 genome

AF:

0.369

AC:

56160

AN:

152104

Hom.:

12119

Cov.:

AF XY:

0.380

AC XY:

28282

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.146

Gnomad4 AMR

AF:

0.424

Gnomad4 ASJ

AF:

0.400

Gnomad4 EAS

AF:

0.609

Gnomad4 SAS

AF:

0.670

Gnomad4 FIN

AF:

0.480

Gnomad4 NFE

AF:

0.434

Gnomad4 OTH

AF:

0.373

Alfa

AF:

0.423

Hom.:

17788

Bravo

AF:

0.351

Asia WGS

AF:

0.636

AC:

2204

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over