chr5-272771-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_013232.4(PDCD6):āc.162C>Gā(p.Asn54Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,584,110 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts 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 (ā ).
Frequency
Consequence
NM_013232.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDCD6 | NM_013232.4 | c.162C>G | p.Asn54Lys | missense_variant, splice_region_variant | 2/6 | ENST00000264933.9 | NP_037364.1 | |
PDCD6-AHRR | NR_165159.2 | n.237C>G | splice_region_variant, non_coding_transcript_exon_variant | 2/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDCD6 | ENST00000264933.9 | c.162C>G | p.Asn54Lys | missense_variant, splice_region_variant | 2/6 | 1 | NM_013232.4 | ENSP00000264933 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000871 AC: 12AN: 137794Hom.: 1 Cov.: 27
GnomAD3 exomes AF: 0.000114 AC: 27AN: 237846Hom.: 3 AF XY: 0.000123 AC XY: 16AN XY: 130030
GnomAD4 exome AF: 0.000155 AC: 224AN: 1446256Hom.: 4 Cov.: 30 AF XY: 0.000145 AC XY: 104AN XY: 719644
GnomAD4 genome AF: 0.0000870 AC: 12AN: 137854Hom.: 1 Cov.: 27 AF XY: 0.0000890 AC XY: 6AN XY: 67426
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.162C>G (p.N54K) alteration is located in exon 2 (coding exon 2) of the PDCD6 gene. This alteration results from a C to G substitution at nucleotide position 162, causing the asparagine (N) at amino acid position 54 to be replaced by a lysine (K). 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