chr19-49862279-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_007254.4(PNKP):c.1032G>A(p.Arg344Arg) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000756 in 1,593,320 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_007254.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00387 AC: 589AN: 152174Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00108 AC: 227AN: 209500Hom.: 2 AF XY: 0.000802 AC XY: 91AN XY: 113430
GnomAD4 exome AF: 0.000418 AC: 603AN: 1441028Hom.: 2 Cov.: 34 AF XY: 0.000362 AC XY: 259AN XY: 715016
GnomAD4 genome AF: 0.00395 AC: 601AN: 152292Hom.: 3 Cov.: 32 AF XY: 0.00377 AC XY: 281AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Inborn genetic diseases Benign:1
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. -
not provided Benign:1
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Developmental and epileptic encephalopathy, 12 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at