chr3-57276621-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142733.3(ASB14):c.1693C>T(p.Arg565Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,613,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001142733.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ASB14 | NM_001142733.3 | c.1693C>T | p.Arg565Cys | missense_variant | 10/11 | ENST00000487349.6 | NP_001136205.2 | |
LOC105377102 | NR_135535.1 | n.342+162G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ASB14 | ENST00000487349.6 | c.1693C>T | p.Arg565Cys | missense_variant | 10/11 | 1 | NM_001142733.3 | ENSP00000419199 | P1 | |
ASB14 | ENST00000515033.1 | n.838C>T | non_coding_transcript_exon_variant | 3/3 | 1 | |||||
APPL1 | ENST00000650354.1 | c.*220+162G>A | intron_variant, NMD_transcript_variant | ENSP00000498115 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152130Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251354Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135850
GnomAD4 exome AF: 0.000164 AC: 239AN: 1461494Hom.: 0 Cov.: 30 AF XY: 0.000157 AC XY: 114AN XY: 727064
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152248Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 8AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.1693C>T (p.R565C) alteration is located in exon 10 (coding exon 9) of the ASB14 gene. This alteration results from a C to T substitution at nucleotide position 1693, causing the arginine (R) at amino acid position 565 to be replaced by a cysteine (C). 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