rs116098879
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_138694.4(PKHD1):c.8673C>T(p.Arg2891=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,346 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R2891R) has been classified as Likely benign.
Frequency
Consequence
NM_138694.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKHD1 | NM_138694.4 | c.8673C>T | p.Arg2891= | synonymous_variant | 56/67 | ENST00000371117.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKHD1 | ENST00000371117.8 | c.8673C>T | p.Arg2891= | synonymous_variant | 56/67 | 1 | NM_138694.4 | P2 | |
PKHD1 | ENST00000340994.4 | c.8673C>T | p.Arg2891= | synonymous_variant | 56/61 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250676Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135444
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461234Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726970
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74290
ClinVar
Submissions by phenotype
Autosomal recessive polycystic kidney disease Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | May 11, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2023 | - - |
Polycystic kidney disease 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at