chr7-150284755-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001164458.2(ACTR3C):c.562A>C(p.Lys188Gln) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000677 in 1,611,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict 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 Uncertain significance (★).
Frequency
Consequence
NM_001164458.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTR3C | NM_001164458.2 | c.562A>C | p.Lys188Gln | missense_variant, splice_region_variant | 6/8 | ENST00000683684.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTR3C | ENST00000683684.1 | c.562A>C | p.Lys188Gln | missense_variant, splice_region_variant | 6/8 | NM_001164458.2 | P1 | ||
ACTR3C | ENST00000252071.8 | c.562A>C | p.Lys188Gln | missense_variant, splice_region_variant | 6/8 | 1 | P1 | ||
ACTR3C | ENST00000478393.5 | c.556A>C | p.Lys186Gln | missense_variant, splice_region_variant | 5/6 | 1 | |||
ACTR3C | ENST00000539352.5 | c.562A>C | p.Lys188Gln | missense_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000125 AC: 31AN: 248234Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 134086
GnomAD4 exome AF: 0.0000576 AC: 84AN: 1458964Hom.: 0 Cov.: 32 AF XY: 0.0000648 AC XY: 47AN XY: 725650
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 28, 2022 | The c.562A>C (p.K188Q) alteration is located in exon 6 (coding exon 5) of the ACTR3C gene. This alteration results from a A to C substitution at nucleotide position 562, causing the lysine (K) at amino acid position 188 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at