6-148440354-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015278.5(SASH1):c.337-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,556 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_015278.5 splice_region, 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 |
---|---|---|---|---|---|---|---|
SASH1 | NM_015278.5 | c.337-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000367467.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SASH1 | ENST00000367467.8 | c.337-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015278.5 | P1 | |||
SASH1 | ENST00000367469.5 | n.255-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 | |||||
SASH1 | ENST00000470750.1 | upstream_gene_variant | 3 | ||||||
SASH1 | ENST00000637469.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 151780Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251378Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135854
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461658Hom.: 0 Cov.: 33 AF XY: 0.0000344 AC XY: 25AN XY: 727132
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 151898Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74200
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 02, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at