rs199572198
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_015488.5(PNKD):āc.350A>Gā(p.Asn117Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000261 in 1,604,394 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_015488.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNKD | NM_015488.5 | c.350A>G | p.Asn117Ser | missense_variant, splice_region_variant | 3/10 | ENST00000273077.9 | |
CATIP-AS2 | NR_125777.1 | n.120+11264T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNKD | ENST00000273077.9 | c.350A>G | p.Asn117Ser | missense_variant, splice_region_variant | 3/10 | 1 | NM_015488.5 | ||
CATIP-AS2 | ENST00000411433.1 | n.120+11264T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 151994Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000882 AC: 214AN: 242704Hom.: 1 AF XY: 0.000625 AC XY: 82AN XY: 131256
GnomAD4 exome AF: 0.000273 AC: 397AN: 1452282Hom.: 1 Cov.: 30 AF XY: 0.000219 AC XY: 158AN XY: 722540
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152112Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74380
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 24, 2020 | - - |
Paroxysmal nonkinesigenic dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at