22-43137099-C-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_173467.5(MCAT):āc.711G>Cā(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 (ā ā ).
Frequency
Genomes: š 0.022 ( 133 hom., cov: 33)
Exomes š: 0.0021 ( 99 hom. )
Consequence
MCAT
NM_173467.5 synonymous
NM_173467.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.488
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
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_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.488 with no splicing effect.
BA1
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MCAT | NM_173467.5 | c.711G>C | p.Val237= | synonymous_variant | 3/4 | ENST00000290429.11 | NP_775738.3 | |
MCAT | NM_014507.3 | c.512-3613G>C | intron_variant | NP_055322.1 | ||||
MCAT | NR_046423.1 | n.595-3613G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCAT | ENST00000290429.11 | c.711G>C | p.Val237= | synonymous_variant | 3/4 | 1 | NM_173467.5 | ENSP00000290429 | P1 | |
MCAT | ENST00000327555.5 | c.512-3613G>C | intron_variant | 1 | ENSP00000331306 |
Frequencies
GnomAD3 genomes AF: 0.0218 AC: 3319AN: 152204Hom.: 131 Cov.: 33
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GnomAD3 exomes AF: 0.00534 AC: 1344AN: 251466Hom.: 55 AF XY: 0.00384 AC XY: 522AN XY: 135912
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GnomAD4 exome AF: 0.00207 AC: 3022AN: 1461826Hom.: 99 Cov.: 31 AF XY: 0.00173 AC XY: 1258AN XY: 727206
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GnomAD4 genome AF: 0.0219 AC: 3338AN: 152322Hom.: 133 Cov.: 33 AF XY: 0.0213 AC XY: 1584AN XY: 74486
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 25, 2018 | - - |
Computational scores
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BayesDel_noAF
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CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at