rs34649849
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_015132.5(SNX13):c.1954-11_1954-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,092,004 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_015132.5 splice_polypyrimidine_tract, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX13 | NM_015132.5 | c.1954-11_1954-9del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000428135.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX13 | ENST00000428135.7 | c.1954-11_1954-9del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015132.5 | P1 | |||
SNX13 | ENST00000611725.4 | c.1987-11_1987-9del | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
SNX13 | ENST00000496855.1 | n.298-11_298-9del | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 1 | |||||
SNX13 | ENST00000409076.6 | c.*1652-11_*1652-9del | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 130362Hom.: 0 Cov.: 0 FAILED QC
GnomAD4 exome AF: 0.000103 AC: 112AN: 1092004Hom.: 0 AF XY: 0.000124 AC XY: 66AN XY: 530932
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 130362Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 62468
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.