rs17398435
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152551.4(SNRNP48):c.717+1129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 152,192 control chromosomes in the GnomAD database, including 302 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.053 ( 302 hom., cov: 33)
Consequence
SNRNP48
NM_152551.4 intron
NM_152551.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.154
Genes affected
SNRNP48 (HGNC:21368): (small nuclear ribonucleoprotein U11/U12 subunit 48) Predicted to enable metal ion binding activity. Predicted to be involved in RNA splicing. Located in cytosol and nucleoplasm. Part of U12-type spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0787 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNRNP48 | NM_152551.4 | c.717+1129G>A | intron_variant | ENST00000342415.6 | |||
SNRNP48 | XM_011514312.4 | c.654+1129G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNRNP48 | ENST00000342415.6 | c.717+1129G>A | intron_variant | 1 | NM_152551.4 | P1 | |||
SNRNP48 | ENST00000634363.1 | c.*275+1129G>A | intron_variant, NMD_transcript_variant | 2 | |||||
SNRNP48 | ENST00000496946.1 | n.1974+1129G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0535 AC: 8139AN: 152074Hom.: 302 Cov.: 33
GnomAD3 genomes
?
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8139
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152074
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0535 AC: 8142AN: 152192Hom.: 302 Cov.: 33 AF XY: 0.0523 AC XY: 3893AN XY: 74420
GnomAD4 genome
?
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AC:
8142
AN:
152192
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33
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3893
AN XY:
74420
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47
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at