rs10275320
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_182762.4(MACC1):c.2347-1273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 152,192 control chromosomes in the GnomAD database, including 918 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 0.10 ( 918 hom., cov: 32)
Consequence
MACC1
NM_182762.4 intron
NM_182762.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.278
Genes affected
MACC1 (HGNC:30215): (MET transcriptional regulator MACC1) MACC1 is a key regulator of the hepatocyte growth factor (HGF; MIM 142409)-HGF receptor (HGFR, or MET; MIM 164860) pathway, which is involved in cellular growth, epithelial-mesenchymal transition, angiogenesis, cell motility, invasiveness, and metastasis. Expression of MACC1 in colon cancer (MIM 114500) specimens is an independent prognostic indicator for metastasis formation and metastasis-free survival (Stein et al., 2009 [PubMed 19098908]).[supplied by OMIM, Mar 2009]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MACC1 | NM_182762.4 | c.2347-1273C>T | intron_variant | ENST00000400331.10 | |||
MACC1-AS1 | NR_046756.1 | n.105+411G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MACC1 | ENST00000400331.10 | c.2347-1273C>T | intron_variant | 2 | NM_182762.4 | P1 | |||
MACC1 | ENST00000332878.8 | c.2347-1273C>T | intron_variant | 1 | P1 | ||||
MACC1-AS1 | ENST00000439285.1 | n.105+411G>A | intron_variant, non_coding_transcript_variant | 3 | |||||
MACC1 | ENST00000589011.1 | c.2347-1273C>T | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0998 AC: 15179AN: 152074Hom.: 917 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0998 AC: 15196AN: 152192Hom.: 918 Cov.: 32 AF XY: 0.0979 AC XY: 7283AN XY: 74408
GnomAD4 genome
?
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15196
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32
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74408
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237
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
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