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
Consequence
NM_030665.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000102 AC: 25AN: 243984Hom.: 0 AF XY: 0.0000751 AC XY: 10AN XY: 133242
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1460266Hom.: 0 Cov.: 36 AF XY: 0.0000853 AC XY: 62AN XY: 726430
GnomAD4 genome AF: 0.000118 AC: 18AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74374
ClinVar
Submissions by phenotype
not provided Pathogenic:1Benign:2
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RAI1: BS2 -
not specified Benign:2
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Autosomal recessive nonsyndromic hearing loss 9 Pathogenic:1
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RAI1-related disorder Uncertain:1
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
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at