2-37279881-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005813.6(PRKD3):āc.1037A>Gā(p.Asn346Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,461,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_005813.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKD3 | NM_005813.6 | c.1037A>G | p.Asn346Ser | missense_variant | 8/19 | ENST00000234179.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKD3 | ENST00000234179.8 | c.1037A>G | p.Asn346Ser | missense_variant | 8/19 | 1 | NM_005813.6 | P1 | |
PRKD3 | ENST00000494667.5 | n.1536A>G | non_coding_transcript_exon_variant | 7/12 | 1 | ||||
PRKD3 | ENST00000379066.5 | c.1037A>G | p.Asn346Ser | missense_variant | 8/19 | 5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250814Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135590
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461042Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726854
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at