9-128691235-T-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003011.4(SET):c.131+8T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000663 in 1,568,138 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003011.4 splice_region, 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 |
---|---|---|---|---|---|---|---|
SET | NM_003011.4 | c.131+8T>G | splice_region_variant, intron_variant | ENST00000322030.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SET | ENST00000322030.13 | c.131+8T>G | splice_region_variant, intron_variant | 1 | NM_003011.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152206Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000707 AC: 17AN: 240322Hom.: 0 AF XY: 0.0000771 AC XY: 10AN XY: 129778
GnomAD4 exome AF: 0.0000537 AC: 76AN: 1415932Hom.: 0 Cov.: 24 AF XY: 0.0000510 AC XY: 36AN XY: 706126
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152206Hom.: 1 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74352
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 18, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at