rs3868143
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001100915.3(KCTD19):c.1590+30A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,494,894 control chromosomes in the GnomAD database, including 18,837 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.22 ( 7686 hom., cov: 32)
Exomes 𝑓: 0.094 ( 11151 hom. )
Consequence
KCTD19
NM_001100915.3 intron
NM_001100915.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.02
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCTD19 | NM_001100915.3 | c.1590+30A>G | intron_variant | ENST00000304372.6 | NP_001094385.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCTD19 | ENST00000304372.6 | c.1590+30A>G | intron_variant | 1 | NM_001100915.3 | ENSP00000305702 | P1 | |||
KCTD19 | ENST00000570049.5 | n.3422+30A>G | intron_variant, non_coding_transcript_variant | 1 | ||||||
KCTD19 | ENST00000566392.5 | n.2859+30A>G | intron_variant, non_coding_transcript_variant | 2 | ||||||
KCTD19 | ENST00000569333.5 | n.3588+30A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.223 AC: 33856AN: 152024Hom.: 7649 Cov.: 32
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GnomAD3 exomes AF: 0.119 AC: 29444AN: 248402Hom.: 3866 AF XY: 0.115 AC XY: 15484AN XY: 134778
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GnomAD4 exome AF: 0.0940 AC: 126188AN: 1342752Hom.: 11151 Cov.: 21 AF XY: 0.0937 AC XY: 63172AN XY: 674108
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GnomAD4 genome AF: 0.223 AC: 33939AN: 152142Hom.: 7686 Cov.: 32 AF XY: 0.221 AC XY: 16466AN XY: 74378
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
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