1-229432190-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001100.4(ACTA1):c.617-5C>T 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 0.000724 in 1,613,432 control chromosomes in the GnomAD database, including 8 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_001100.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTA1 | NM_001100.4 | c.617-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000366684.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTA1 | ENST00000366684.7 | c.617-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001100.4 | P1 | |||
ACTA1 | ENST00000366683.4 | c.617-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
ACTA1 | ENST00000684723.1 | c.482-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Frequencies
GnomAD3 genomes AF: 0.00364 AC: 554AN: 152134Hom.: 3 Cov.: 31
GnomAD3 exomes AF: 0.000939 AC: 234AN: 249312Hom.: 0 AF XY: 0.000689 AC XY: 93AN XY: 135068
GnomAD4 exome AF: 0.000420 AC: 613AN: 1461180Hom.: 5 Cov.: 34 AF XY: 0.000387 AC XY: 281AN XY: 726886
GnomAD4 genome AF: 0.00365 AC: 555AN: 152252Hom.: 3 Cov.: 31 AF XY: 0.00347 AC XY: 258AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Actin accumulation myopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 07, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at