chr3-43303248-A-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_017719.5(SNRK):āc.45A>Gā(p.Leu15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00444 in 1,614,148 control chromosomes in the GnomAD database, including 298 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.024 ( 148 hom., cov: 32)
Exomes š: 0.0025 ( 150 hom. )
Consequence
SNRK
NM_017719.5 synonymous
NM_017719.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.670
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 3-43303248-A-G is Benign according to our data. Variant chr3-43303248-A-G is described in ClinVar as [Benign]. Clinvar id is 791918.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.67 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0786 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNRK | NM_017719.5 | c.45A>G | p.Leu15= | synonymous_variant | 3/7 | ENST00000296088.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNRK | ENST00000296088.12 | c.45A>G | p.Leu15= | synonymous_variant | 3/7 | 1 | NM_017719.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0235 AC: 3575AN: 152176Hom.: 147 Cov.: 32
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GnomAD3 exomes AF: 0.00603 AC: 1503AN: 249274Hom.: 71 AF XY: 0.00461 AC XY: 623AN XY: 135250
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GnomAD4 exome AF: 0.00246 AC: 3592AN: 1461854Hom.: 150 Cov.: 31 AF XY: 0.00211 AC XY: 1532AN XY: 727220
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GnomAD4 genome AF: 0.0235 AC: 3582AN: 152294Hom.: 148 Cov.: 32 AF XY: 0.0227 AC XY: 1691AN XY: 74480
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
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CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at