chr14-29577305-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002742.3(PRKD1):c.2672A>G(p.His891Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 1,613,844 control chromosomes in the GnomAD database, including 144 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002742.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKD1 | NM_002742.3 | c.2672A>G | p.His891Arg | missense_variant | 18/18 | ENST00000331968.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKD1 | ENST00000331968.11 | c.2672A>G | p.His891Arg | missense_variant | 18/18 | 1 | NM_002742.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0112 AC: 1697AN: 152138Hom.: 28 Cov.: 32
GnomAD3 exomes AF: 0.0120 AC: 3013AN: 250974Hom.: 30 AF XY: 0.0125 AC XY: 1699AN XY: 135596
GnomAD4 exome AF: 0.0106 AC: 15553AN: 1461588Hom.: 116 Cov.: 31 AF XY: 0.0106 AC XY: 7726AN XY: 727098
GnomAD4 genome ? AF: 0.0111 AC: 1697AN: 152256Hom.: 28 Cov.: 32 AF XY: 0.0123 AC XY: 912AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | PRKD1: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at