chr19-38706095-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 3P and 20B. PM1PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_004924.6(ACTN4):c.536C>T(p.Pro179Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000445 in 1,614,132 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P179P) has been classified as Benign.
Frequency
Consequence
NM_004924.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTN4 | NM_004924.6 | c.536C>T | p.Pro179Leu | missense_variant | 5/21 | ENST00000252699.7 | |
LOC107985291 | XR_001753937.2 | n.170-3931G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTN4 | ENST00000252699.7 | c.536C>T | p.Pro179Leu | missense_variant | 5/21 | 1 | NM_004924.6 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00253 AC: 385AN: 152182Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000608 AC: 153AN: 251474Hom.: 0 AF XY: 0.000375 AC XY: 51AN XY: 135918
GnomAD4 exome AF: 0.000227 AC: 332AN: 1461832Hom.: 0 Cov.: 30 AF XY: 0.000193 AC XY: 140AN XY: 727218
GnomAD4 genome AF: 0.00254 AC: 387AN: 152300Hom.: 3 Cov.: 33 AF XY: 0.00222 AC XY: 165AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 05, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | ACTN4: PP2, PP3, BS2 - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 22, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Focal segmental glomerulosclerosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jul 01, 2020 | - - |
Focal segmental glomerulosclerosis 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at