chr18-23530033-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_013326.5(RMC1):c.1500C>T(p.Tyr500=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00647 in 1,613,348 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0059 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0065 ( 60 hom. )
Consequence
RMC1
NM_013326.5 synonymous
NM_013326.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.15
Genes affected
RMC1 (HGNC:24326): (regulator of MON1-CCZ1) This gene encodes a colon cancer associated protein. [provided by RefSeq, Jan 2013]
NPC1 (HGNC:7897): (NPC intracellular cholesterol transporter 1) This gene encodes a large protein that resides in the limiting membrane of endosomes and lysosomes and mediates intracellular cholesterol trafficking via binding of cholesterol to its N-terminal domain. It is predicted to have a cytoplasmic C-terminus, 13 transmembrane domains, and 3 large loops in the lumen of the endosome - the last loop being at the N-terminus. This protein transports low-density lipoproteins to late endosomal/lysosomal compartments where they are hydrolized and released as free cholesterol. Defects in this gene cause Niemann-Pick type C disease, a rare autosomal recessive neurodegenerative disorder characterized by over accumulation of cholesterol and glycosphingolipids in late endosomal/lysosomal compartments.[provided by RefSeq, Aug 2009]
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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=-0.56).
BP6
Variant 18-23530033-C-T is Benign according to our data. Variant chr18-23530033-C-T is described in ClinVar as [Benign]. Clinvar id is 781357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.15 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00653 (9542/1461044) while in subpopulation MID AF= 0.0246 (142/5766). AF 95% confidence interval is 0.0213. There are 60 homozygotes in gnomad4_exome. There are 5038 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 902 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RMC1 | NM_013326.5 | c.1500C>T | p.Tyr500= | synonymous_variant | 17/20 | ENST00000269221.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RMC1 | ENST00000269221.8 | c.1500C>T | p.Tyr500= | synonymous_variant | 17/20 | 1 | NM_013326.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00590 AC: 898AN: 152186Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00827 AC: 2080AN: 251402Hom.: 15 AF XY: 0.00896 AC XY: 1218AN XY: 135880
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GnomAD4 exome AF: 0.00653 AC: 9542AN: 1461044Hom.: 60 Cov.: 32 AF XY: 0.00693 AC XY: 5038AN XY: 726896
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GnomAD4 genome AF: 0.00592 AC: 902AN: 152304Hom.: 3 Cov.: 32 AF XY: 0.00679 AC XY: 506AN XY: 74474
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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 | Invitae | Mar 29, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at