rs13447397
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001101.5(ACTB):c.124-4C>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 0.000216 in 1,613,960 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 Benign (★★).
Frequency
Consequence
NM_001101.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACTB | NM_001101.5 | c.124-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000646664.1 | NP_001092.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACTB | ENST00000646664.1 | c.124-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001101.5 | ENSP00000494750 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00106 AC: 267AN: 251256Hom.: 0 AF XY: 0.000714 AC XY: 97AN XY: 135846
GnomAD4 exome AF: 0.000218 AC: 319AN: 1461608Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 127AN XY: 727112
GnomAD4 genome AF: 0.000190 AC: 29AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74500
ClinVar
Submissions by phenotype
Baraitser-Winter syndrome 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
ACTB-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 05, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Developmental malformations-deafness-dystonia syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 09, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at