chr3-51663239-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015106.4(RAD54L2):āc.4223A>Gā(p.Asn1408Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,613,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015106.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151532Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251178Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135740
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461712Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727138
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151532Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 73960
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4223A>G (p.N1408S) alteration is located in exon 22 (coding exon 21) of the RAD54L2 gene. This alteration results from a A to G substitution at nucleotide position 4223, causing the asparagine (N) at amino acid position 1408 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at