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GeneBe

22-43137099-C-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_173467.5(MCAT):c.711G>C(p.Val237=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00394 in 1,614,148 control chromosomes in the GnomAD database, including 232 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.022 ( 133 hom., cov: 33)
Exomes 𝑓: 0.0021 ( 99 hom. )

Consequence

MCAT
NM_173467.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.488
Variant links:
Genes affected
MCAT (HGNC:29622): (malonyl-CoA-acyl carrier protein transacylase) The protein encoded by this gene is found exclusively in the mitochondrion, where it catalyzes the transfer of a malonyl group from malonyl-CoA to the mitochondrial acyl carrier protein. The encoded protein may be part of a fatty acid synthase complex that is more like the type II prokaryotic and plastid complexes rather than the type I human cytosolic complex. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 22-43137099-C-G is Benign according to our data. Variant chr22-43137099-C-G is described in ClinVar as [Benign]. Clinvar id is 786385.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.488 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0749 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MCATNM_173467.5 linkuse as main transcriptc.711G>C p.Val237= synonymous_variant 3/4 ENST00000290429.11
MCATNM_014507.3 linkuse as main transcriptc.512-3613G>C intron_variant
MCATNR_046423.1 linkuse as main transcriptn.595-3613G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MCATENST00000290429.11 linkuse as main transcriptc.711G>C p.Val237= synonymous_variant 3/41 NM_173467.5 P1Q8IVS2-1
MCATENST00000327555.5 linkuse as main transcriptc.512-3613G>C intron_variant 1 Q8IVS2-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0218
AC:
3319
AN:
152204
Hom.:
131
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0769
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00569
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.0129
GnomAD3 exomes
AF:
0.00534
AC:
1344
AN:
251466
Hom.:
55
AF XY:
0.00384
AC XY:
522
AN XY:
135912
show subpopulations
Gnomad AFR exome
AF:
0.0745
Gnomad AMR exome
AF:
0.00283
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000132
Gnomad OTH exome
AF:
0.00244
GnomAD4 exome
AF:
0.00207
AC:
3022
AN:
1461826
Hom.:
99
Cov.:
31
AF XY:
0.00173
AC XY:
1258
AN XY:
727206
show subpopulations
Gnomad4 AFR exome
AF:
0.0754
Gnomad4 AMR exome
AF:
0.00335
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000197
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000513
Gnomad4 OTH exome
AF:
0.00432
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0219
AC:
3338
AN:
152322
Hom.:
133
Cov.:
33
AF XY:
0.0213
AC XY:
1584
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.0771
Gnomad4 AMR
AF:
0.00568
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.0128
Alfa
AF:
0.00633
Hom.:
14
Bravo
AF:
0.0242
Asia WGS
AF:
0.00577
AC:
20
AN:
3478
EpiCase
AF:
0.00
EpiControl
AF:
0.000237

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 submitterclinical testingInvitaeFeb 25, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
Cadd
Benign
4.2
Dann
Benign
0.83

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: rs73886407; hg19: chr22-43533105; API