chr10-104254967-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_004832.3(GSTO1):c.34+5G>A variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00233 in 1,607,418 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004832.3 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTO1 | NM_004832.3 | c.34+5G>A | splice_donor_5th_base_variant, intron_variant | ENST00000369713.10 | |||
LOC124902497 | XR_007062284.1 | n.366-6375C>T | intron_variant, non_coding_transcript_variant | ||||
GSTO1 | NM_001191002.2 | c.34+5G>A | splice_donor_5th_base_variant, intron_variant | ||||
GSTO1 | NM_001191003.2 | c.-50-196G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTO1 | ENST00000369713.10 | c.34+5G>A | splice_donor_5th_base_variant, intron_variant | 1 | NM_004832.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0121 AC: 1847AN: 152046Hom.: 27 Cov.: 32
GnomAD3 exomes AF: 0.00297 AC: 687AN: 231524Hom.: 14 AF XY: 0.00230 AC XY: 291AN XY: 126334
GnomAD4 exome AF: 0.00130 AC: 1896AN: 1455254Hom.: 37 Cov.: 31 AF XY: 0.00109 AC XY: 786AN XY: 723598
GnomAD4 genome ? AF: 0.0122 AC: 1851AN: 152164Hom.: 27 Cov.: 32 AF XY: 0.0120 AC XY: 892AN XY: 74386
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at