rs2024092
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014963.3(SBNO2):c.442-10C>T 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 0.219 in 1,607,266 control chromosomes in the GnomAD database, including 40,373 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
Consequence
NM_014963.3 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SBNO2 | NM_014963.3 | c.442-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000361757.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBNO2 | ENST00000361757.8 | c.442-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014963.3 | P2 | |||
SBNO2 | ENST00000592222.5 | n.295-10C>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 1 | |||||
SBNO2 | ENST00000438103.6 | c.271-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 2 | A2 | ||||
SBNO2 | ENST00000587024.5 | c.442-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.253 AC: 38471AN: 151964Hom.: 5092 Cov.: 32
GnomAD3 exomes AF: 0.242 AC: 57574AN: 238154Hom.: 7423 AF XY: 0.235 AC XY: 30478AN XY: 129784
GnomAD4 exome AF: 0.215 AC: 313586AN: 1455184Hom.: 35275 Cov.: 34 AF XY: 0.215 AC XY: 155906AN XY: 723490
GnomAD4 genome ? AF: 0.253 AC: 38504AN: 152082Hom.: 5098 Cov.: 32 AF XY: 0.256 AC XY: 19033AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at