chr17-81510547-C-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001614.5(ACTG1):c.*143G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,046,454 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00064 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000081 ( 0 hom. )
Consequence
ACTG1
NM_001614.5 3_prime_UTR
NM_001614.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.653
Genes affected
ACTG1 (HGNC:144): (actin gamma 1) Actins are highly conserved proteins that are involved in various types of cell motility and in maintenance of the cytoskeleton. Three main groups of actin isoforms have been identified in vertebrate animals: alpha, beta, and gamma. The alpha actins are found in muscle tissues and are a major constituent of the contractile apparatus. The beta and gamma actins co-exist in most cell types as components of the cytoskeleton and as mediators of internal cell motility. Actin gamma 1, encoded by this gene, is a cytoplasmic actin found in all cell types. Mutations in this gene are associated with DFNA20/26, a subtype of autosomal dominant non-syndromic sensorineural progressive hearing loss and also with Baraitser-Winter syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 17-81510547-C-G is Benign according to our data. Variant chr17-81510547-C-G is described in ClinVar as [Benign]. Clinvar id is 1264887.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000643 (98/152362) while in subpopulation AFR AF= 0.00219 (91/41580). AF 95% confidence interval is 0.00183. There are 0 homozygotes in gnomad4. There are 49 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 98 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTG1 | NM_001614.5 | c.*143G>C | 3_prime_UTR_variant | 6/6 | ENST00000573283.7 | ||
ACTG1 | NM_001199954.3 | c.*143G>C | 3_prime_UTR_variant | 6/6 | |||
ACTG1 | NR_037688.3 | n.1343G>C | non_coding_transcript_exon_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTG1 | ENST00000573283.7 | c.*143G>C | 3_prime_UTR_variant | 6/6 | 5 | NM_001614.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000644 AC: 98AN: 152244Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000107 AC: 20AN: 187380Hom.: 0 AF XY: 0.0000881 AC XY: 9AN XY: 102112
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GnomAD4 exome AF: 0.0000805 AC: 72AN: 894092Hom.: 0 Cov.: 12 AF XY: 0.0000625 AC XY: 29AN XY: 464046
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GnomAD4 genome AF: 0.000643 AC: 98AN: 152362Hom.: 0 Cov.: 32 AF XY: 0.000658 AC XY: 49AN XY: 74498
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 06, 2020 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at