4-88008153-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_000297.4(PKD2):āc.420G>Cā(p.Gly140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000763 in 1,311,170 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G140G) has been classified as Benign.
Frequency
Consequence
NM_000297.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD2 | NM_000297.4 | c.420G>C | p.Gly140= | synonymous_variant | 1/15 | ENST00000237596.7 | |
PKD2 | XM_011532028.3 | c.420G>C | p.Gly140= | synonymous_variant | 1/14 | ||
PKD2 | NR_156488.2 | n.519G>C | non_coding_transcript_exon_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD2 | ENST00000237596.7 | c.420G>C | p.Gly140= | synonymous_variant | 1/15 | 1 | NM_000297.4 | P1 | |
ENST00000662475.1 | n.112+213C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000118 AC: 1AN: 84630Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 48146
GnomAD4 exome AF: 7.63e-7 AC: 1AN: 1311170Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 646148
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at