rs13447394
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001101.5(ACTB):c.-6-4G>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 0.00464 in 1,610,772 control chromosomes in the GnomAD database, including 24 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 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 | UniProt |
---|---|---|---|---|---|---|---|
ACTB | NM_001101.5 | c.-6-4G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000646664.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTB | ENST00000646664.1 | c.-6-4G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001101.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00318 AC: 484AN: 152184Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00303 AC: 737AN: 243158Hom.: 4 AF XY: 0.00302 AC XY: 403AN XY: 133468
GnomAD4 exome AF: 0.00479 AC: 6985AN: 1458470Hom.: 23 Cov.: 32 AF XY: 0.00466 AC XY: 3382AN XY: 725636
GnomAD4 genome ? AF: 0.00318 AC: 484AN: 152302Hom.: 1 Cov.: 33 AF XY: 0.00286 AC XY: 213AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 17, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 02, 2017 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | ACTB: BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 22, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Baraitser-Winter syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Developmental malformations-deafness-dystonia syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at