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GeneBe

rs10838738

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014342.4(MTCH2):c.87+882T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,066 control chromosomes in the GnomAD database, including 7,004 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 0.28 ( 7004 hom., cov: 32)

Consequence

MTCH2
NM_014342.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.179
Variant links:
Genes affected
MTCH2 (HGNC:17587): (mitochondrial carrier 2) This gene encodes a member of the SLC25 family of nuclear-encoded transporters that are localized in the inner mitochondrial membrane. Members of this superfamily are involved in many metabolic pathways and cell functions. Genome-wide association studies in human have identified single-nucleotide polymorphisms in several loci associated with obesity. This gene is one such locus, which is highly expressed in white adipose tissue and adipocytes, and thought to play a regulatory role in adipocyte differentiation and biology. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. A recent study showed this gene to be an authentic stop codon readthrough target that can produce two isoforms from the same mRNA by use of alternative in-frame translation termination codons. [provided by RefSeq, Dec 2017]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MTCH2NM_014342.4 linkuse as main transcriptc.87+882T>C intron_variant ENST00000302503.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MTCH2ENST00000302503.8 linkuse as main transcriptc.87+882T>C intron_variant 1 NM_014342.4 P1
MTCH2ENST00000530428.2 linkuse as main transcriptc.87+882T>C intron_variant 5
MTCH2ENST00000533571.2 linkuse as main transcriptn.134+904T>C intron_variant, non_coding_transcript_variant 2
MTCH2ENST00000539759.5 linkuse as main transcriptn.74+882T>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.280
AC:
42562
AN:
151946
Hom.:
6992
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0928
Gnomad AMI
AF:
0.637
Gnomad AMR
AF:
0.366
Gnomad ASJ
AF:
0.292
Gnomad EAS
AF:
0.310
Gnomad SAS
AF:
0.301
Gnomad FIN
AF:
0.345
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.355
Gnomad OTH
AF:
0.297
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.280
AC:
42586
AN:
152066
Hom.:
7004
Cov.:
32
AF XY:
0.281
AC XY:
20915
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.0926
Gnomad4 AMR
AF:
0.366
Gnomad4 ASJ
AF:
0.292
Gnomad4 EAS
AF:
0.310
Gnomad4 SAS
AF:
0.301
Gnomad4 FIN
AF:
0.345
Gnomad4 NFE
AF:
0.355
Gnomad4 OTH
AF:
0.305
Alfa
AF:
0.341
Hom.:
19674
Bravo
AF:
0.275
Asia WGS
AF:
0.295
AC:
1028
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
3.6
Dann
Benign
0.40

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.

Other links and lift over

dbSNP: rs10838738; hg19: chr11-47663049; API