15-101284975-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003090.4(SNRPA1):c.701G>A(p.Arg234His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,611,888 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R234C) has been classified as Uncertain significance.
Frequency
Consequence
NM_003090.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNRPA1 | NM_003090.4 | c.701G>A | p.Arg234His | missense_variant | Exon 8 of 9 | ENST00000254193.11 | NP_003081.2 | |
SNRPA1 | NR_135506.2 | n.464G>A | non_coding_transcript_exon_variant | Exon 5 of 6 | ||||
SNRPA1 | NR_135507.2 | n.417G>A | non_coding_transcript_exon_variant | Exon 4 of 5 | ||||
SNRPA1 | NR_135508.2 | n.691G>A | non_coding_transcript_exon_variant | Exon 7 of 8 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251410Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135882
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1459656Hom.: 0 Cov.: 29 AF XY: 0.0000138 AC XY: 10AN XY: 726234
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.701G>A (p.R234H) alteration is located in exon 8 (coding exon 8) of the SNRPA1 gene. This alteration results from a G to A substitution at nucleotide position 701, causing the arginine (R) at amino acid position 234 to be replaced by a histidine (H). 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