10-103400496-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014976.2(PDCD11):c.202G>A(p.Ala68Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014976.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDCD11 | NM_014976.2 | c.202G>A | p.Ala68Thr | missense_variant | 3/36 | ENST00000369797.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDCD11 | ENST00000369797.8 | c.202G>A | p.Ala68Thr | missense_variant | 3/36 | 1 | NM_014976.2 | P4 | |
PDCD11 | ENST00000649849.1 | c.202G>A | p.Ala68Thr | missense_variant | 3/36 | A1 | |||
PDCD11 | ENST00000493610.2 | c.*269G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251348Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135840
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1461612Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727092
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74462
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at