rs755572135

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2

The NM_030665.4(RAI1):​c.5254G>A​(p.Gly1752Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000874 in 1,612,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000084 ( 0 hom. )

Consequence

RAI1
NM_030665.4 missense

Scores

5
14

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts P:2U:1B:5

Conservation

PhyloP100: 2.21
Variant links:
Genes affected
RAI1 (HGNC:9834): (retinoic acid induced 1) This gene is located within the Smith-Magenis syndrome region on chromosome 17. It is highly similar to its mouse counterpart and is expressed at high levels mainly in neuronal tissues. The protein encoded by this gene includes a polymorphic polyglutamine tract in the N-terminal domain. Expression of the mouse counterpart in neurons is induced by retinoic acid. This gene is associated with both the severity of the phenotype and the response to medication in schizophrenic patients. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.19183397).
BP6
Variant 17-17798202-G-A is Benign according to our data. Variant chr17-17798202-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 212012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000118 (18/152224) while in subpopulation AMR AF= 0.000196 (3/15286). AF 95% confidence interval is 0.000102. There are 0 homozygotes in gnomad4. There are 11 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 18 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RAI1NM_030665.4 linkc.5254G>A p.Gly1752Arg missense_variant Exon 3 of 6 ENST00000353383.6 NP_109590.3 Q7Z5J4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RAI1ENST00000353383.6 linkc.5254G>A p.Gly1752Arg missense_variant Exon 3 of 6 1 NM_030665.4 ENSP00000323074.4 Q7Z5J4-1
RAI1ENST00000583166.1 linkc.-183G>A upstream_gene_variant 2 ENSP00000463984.1 J3QR08

Frequencies

GnomAD3 genomes
AF:
0.000118
AC:
18
AN:
152224
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000102
AC:
25
AN:
243984
Hom.:
0
AF XY:
0.0000751
AC XY:
10
AN XY:
133242
show subpopulations
Gnomad AFR exome
AF:
0.000133
Gnomad AMR exome
AF:
0.0000291
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000551
Gnomad SAS exome
AF:
0.0000983
Gnomad FIN exome
AF:
0.0000938
Gnomad NFE exome
AF:
0.000138
Gnomad OTH exome
AF:
0.000167
GnomAD4 exome
AF:
0.0000842
AC:
123
AN:
1460266
Hom.:
0
Cov.:
36
AF XY:
0.0000853
AC XY:
62
AN XY:
726430
show subpopulations
Gnomad4 AFR exome
AF:
0.0000597
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.0000383
Gnomad4 NFE exome
AF:
0.0000908
Gnomad4 OTH exome
AF:
0.000149
GnomAD4 genome
AF:
0.000118
AC:
18
AN:
152224
Hom.:
0
Cov.:
33
AF XY:
0.000148
AC XY:
11
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000123
Hom.:
0
Bravo
AF:
0.0000869
ExAC
AF:
0.0000908
AC:
11
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Significance: Likely benign
Submissions summary: Pathogenic:2Uncertain:1Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Pathogenic:1Benign:2
Dec 16, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Nov 03, 2021
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Significance: Likely pathogenic
Review Status: flagged submission
Collection Method: clinical testing

- -

Feb 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

RAI1: BS2 -

not specified Benign:2
Jan 28, 2016
Eurofins Ntd Llc (ga)
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Feb 25, 2015
Genetic Services Laboratory, University of Chicago
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Autosomal recessive nonsyndromic hearing loss 9 Pathogenic:1
-
University of Arizona Genetics Core, University of Arizona
Significance: Pathogenic
Review Status: flagged submission
Collection Method: research

- -

RAI1-related disorder Uncertain:1
Jul 29, 2024
PreventionGenetics, part of Exact Sciences
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: clinical testing

The RAI1 c.5254G>A variant is predicted to result in the amino acid substitution p.Gly1752Arg. This variant has been reported in the homozygous state in four Altaian families with non-syndromic hearing loss; however, none of the patients described in this study manifested specific traits typical for Smith-Magenis syndrome (Families #38, #40, #42, and #43 in Fig 1, Сhurbanov et al. 2016. PubMed ID: 27082237). This variant is reported in 0.014% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Inborn genetic diseases Benign:1
Mar 14, 2024
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.32
CADD
Benign
21
DANN
Uncertain
1.0
DEOGEN2
Benign
0.19
T;.
Eigen
Benign
0.034
Eigen_PC
Benign
-0.017
FATHMM_MKL
Benign
0.64
D
LIST_S2
Benign
0.84
T;T
M_CAP
Benign
0.075
D
MetaRNN
Benign
0.19
T;T
MetaSVM
Benign
-0.70
T
MutationAssessor
Benign
1.1
L;.
PrimateAI
Uncertain
0.65
T
PROVEAN
Uncertain
-2.5
N;.
REVEL
Benign
0.11
Sift
Uncertain
0.0020
D;.
Sift4G
Uncertain
0.024
D;.
Polyphen
0.99
D;.
Vest4
0.74
MutPred
0.28
Gain of solvent accessibility (P = 0.0023);.;
MVP
0.12
MPC
0.68
ClinPred
0.32
T
GERP RS
3.6
Varity_R
0.22
gMVP
0.38

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: rs755572135; hg19: chr17-17701516; COSMIC: COSV55395431; COSMIC: COSV55395431; API