rs189345248
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_138694.4(PKHD1):c.657C>T(p.Gly219=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000941 in 1,594,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. G219G) has been classified as Pathogenic.
Frequency
Consequence
NM_138694.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKHD1 | NM_138694.4 | c.657C>T | p.Gly219= | synonymous_variant | 9/67 | ENST00000371117.8 | |
LOC124901327 | XR_007059606.1 | n.14G>A | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKHD1 | ENST00000371117.8 | c.657C>T | p.Gly219= | synonymous_variant | 9/67 | 1 | NM_138694.4 | P2 | |
PKHD1 | ENST00000340994.4 | c.657C>T | p.Gly219= | synonymous_variant | 9/61 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151936Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250874Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135562
GnomAD4 exome AF: 0.00000971 AC: 14AN: 1442396Hom.: 0 Cov.: 28 AF XY: 0.0000125 AC XY: 9AN XY: 718934
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151936Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 74206
ClinVar
Submissions by phenotype
Autosomal recessive polycystic kidney disease Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Dec 07, 2017 | - - |
Polycystic kidney disease 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at