15-34794648-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005159.5(ACTC1):c.129+32C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00212 in 1,604,810 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005159.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACTC1 | ENST00000290378.6 | c.129+32C>A | intron_variant | Intron 2 of 6 | 1 | NM_005159.5 | ENSP00000290378.4 | |||
GJD2-DT | ENST00000503496.6 | n.300-15848G>T | intron_variant | Intron 2 of 2 | 2 | |||||
ACTC1 | ENST00000560563.2 | n.235+32C>A | intron_variant | Intron 2 of 5 | 2 | |||||
GJD2-DT | ENST00000671663.1 | n.95-15848G>T | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.0107 AC: 1630AN: 151830Hom.: 39 Cov.: 32
GnomAD3 exomes AF: 0.00274 AC: 642AN: 234502Hom.: 11 AF XY: 0.00217 AC XY: 279AN XY: 128596
GnomAD4 exome AF: 0.00122 AC: 1771AN: 1452866Hom.: 31 Cov.: 31 AF XY: 0.00109 AC XY: 786AN XY: 721722
GnomAD4 genome AF: 0.0107 AC: 1631AN: 151944Hom.: 39 Cov.: 32 AF XY: 0.0106 AC XY: 787AN XY: 74308
ClinVar
Submissions by phenotype
not specified Benign:1
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not provided Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at