rs201279208
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001614.5(ACTG1):c.124-8C>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 0.000379 in 1,613,506 control chromosomes in the GnomAD database, including 6 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_001614.5 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 |
---|---|---|---|---|---|---|---|
ACTG1 | NM_001614.5 | c.124-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000573283.7 | |||
ACTG1 | NM_001199954.3 | c.124-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ACTG1 | NR_037688.3 | n.196-8C>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.124-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001614.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000810 AC: 203AN: 250654Hom.: 3 AF XY: 0.000995 AC XY: 135AN XY: 135694
GnomAD4 exome AF: 0.000398 AC: 581AN: 1461230Hom.: 6 Cov.: 37 AF XY: 0.000547 AC XY: 398AN XY: 726942
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 01, 2015 | c.124-8C>T in intron 2 of ACTG1: This variant is not expected to have clinical significance because it has been identified in 0.6% (105/16508) of South Asian c hromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute .org; dbSNP rs201279208). In addition, a C>T change at this position does not di verge from the splice consensus sequence and is therefore unlikely to impact spl icing. - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 14, 2018 | - - |
Autosomal dominant nonsyndromic hearing loss 20 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 | Oct 02, 2018 | - - |
Baraitser-winter syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Autosomal dominant nonsyndromic hearing loss 20;C3281235:Baraitser-winter syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at