chr17-17794419-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_030665.4(RAI1):c.1471G>A(p.Glu491Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_030665.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248102Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134950
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460596Hom.: 0 Cov.: 95 AF XY: 0.00000688 AC XY: 5AN XY: 726608
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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not specified Uncertain:1
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RAI1-related disorder Uncertain:1
The RAI1 c.1471G>A variant is predicted to result in the amino acid substitution p.Glu491Lys. This variant was reported to have occurred de novo in an individual with a developmental disorder (Supplementary Table 1, McRae et al 2017. PubMed ID: 28135719). This variant is reported in 0.0065% of alleles in individuals of South Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Smith-Magenis syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at