chr18-23530033-C-T

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.15
Variant links:
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
RMC1NM_013326.5 linkuse as main transcriptc.1500C>T p.Tyr500= synonymous_variant 17/20 ENST00000269221.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RMC1ENST00000269221.8 linkuse as main transcriptc.1500C>T p.Tyr500= synonymous_variant 17/201 NM_013326.5 P1

Frequencies

GnomAD3 genomes
AF:
0.00590
AC:
898
AN:
152186
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00125
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.00380
Gnomad ASJ
AF:
0.0179
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.0112
Gnomad FIN
AF:
0.0216
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.00609
Gnomad OTH
AF:
0.0110
GnomAD3 exomes
AF:
0.00827
AC:
2080
AN:
251402
Hom.:
15
AF XY:
0.00896
AC XY:
1218
AN XY:
135880
show subpopulations
Gnomad AFR exome
AF:
0.00117
Gnomad AMR exome
AF:
0.00301
Gnomad ASJ exome
AF:
0.0173
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0141
Gnomad FIN exome
AF:
0.0215
Gnomad NFE exome
AF:
0.00718
Gnomad OTH exome
AF:
0.0108
GnomAD4 exome
AF:
0.00653
AC:
9542
AN:
1461044
Hom.:
60
Cov.:
32
AF XY:
0.00693
AC XY:
5038
AN XY:
726896
show subpopulations
Gnomad4 AFR exome
AF:
0.00164
Gnomad4 AMR exome
AF:
0.00309
Gnomad4 ASJ exome
AF:
0.0183
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0134
Gnomad4 FIN exome
AF:
0.0219
Gnomad4 NFE exome
AF:
0.00531
Gnomad4 OTH exome
AF:
0.00827
GnomAD4 genome
AF:
0.00592
AC:
902
AN:
152304
Hom.:
3
Cov.:
32
AF XY:
0.00679
AC XY:
506
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.00132
Gnomad4 AMR
AF:
0.00379
Gnomad4 ASJ
AF:
0.0179
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0114
Gnomad4 FIN
AF:
0.0216
Gnomad4 NFE
AF:
0.00609
Gnomad4 OTH
AF:
0.0109
Alfa
AF:
0.00669
Hom.:
9
Bravo
AF:
0.00419
Asia WGS
AF:
0.00549
AC:
19
AN:
3478
EpiCase
AF:
0.00796
EpiControl
AF:
0.00723

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 testingInvitaeMar 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
CADD
Benign
6.3
DANN
Benign
0.67

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: rs34136453; hg19: chr18-21109997; API