rs150136833
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001614.5(ACTG1):c.803-7C>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 0.0000483 in 1,613,952 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_001614.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTG1 | NM_001614.5 | c.803-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000573283.7 | |||
ACTG1 | NM_001199954.3 | c.803-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ACTG1 | NR_037688.3 | n.875-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTG1 | ENST00000573283.7 | c.803-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001614.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251356Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135892
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461642Hom.: 0 Cov.: 37 AF XY: 0.0000385 AC XY: 28AN XY: 727140
GnomAD4 genome AF: 0.000112 AC: 17AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74478
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 18, 2017 | c.803-7C>T in intron 4 of ACTG1: This variant is not expected to have clinical s ignificance because a C>T change at this position does not diverge from the spli ce consensus sequence and is therefore unlikely to impact splicing. It has been identified in 19/277127 total chromosomes by the genome Aggregation Database (gn omAD, http://gnomad.broadinstitute.org/; dbSNP rs150136833). - |
ACTG1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 14, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Autosomal dominant nonsyndromic hearing loss 20;C3281235:Baraitser-winter syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at