chr11-126205582-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032795.3(RPUSD4):c.682G>A(p.Asp228Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000712 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032795.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPUSD4 | NM_032795.3 | c.682G>A | p.Asp228Asn | missense_variant | Exon 5 of 7 | ENST00000298317.9 | NP_116184.2 | |
RPUSD4 | NM_001363516.2 | c.682G>A | p.Asp228Asn | missense_variant | Exon 5 of 7 | NP_001350445.1 | ||
RPUSD4 | XM_011543039.3 | c.103G>A | p.Asp35Asn | missense_variant | Exon 3 of 5 | XP_011541341.1 | ||
RPUSD4 | NM_001144827.2 | c.632-43G>A | intron_variant | Intron 4 of 6 | NP_001138299.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251412Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135878
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461810Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 727212
GnomAD4 genome AF: 0.000105 AC: 16AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74388
ClinVar
Submissions by phenotype
not specified 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