5-306723-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_013232.4(PDCD6):c.330C>G(p.Ile110Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013232.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDCD6 | ENST00000264933.9 | c.330C>G | p.Ile110Met | missense_variant | Exon 4 of 6 | 1 | NM_013232.4 | ENSP00000264933.4 | ||
ENSG00000286001 | ENST00000651543.1 | n.*1700C>G | non_coding_transcript_exon_variant | Exon 21 of 24 | ENSP00000499215.1 | |||||
ENSG00000286001 | ENST00000651543.1 | n.*1700C>G | 3_prime_UTR_variant | Exon 21 of 24 | ENSP00000499215.1 | |||||
PDCD6-AHRR | ENST00000675395.1 | n.208+2502C>G | intron_variant | Intron 3 of 13 | ENSP00000502570.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251398Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135916
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461706Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727152
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.330C>G (p.I110M) alteration is located in exon 4 (coding exon 4) of the PDCD6 gene. This alteration results from a C to G substitution at nucleotide position 330, causing the isoleucine (I) at amino acid position 110 to be replaced by a methionine (M). 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