rs10502088
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152434.3(CWF19L2):c.1617+5962A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 152,144 control chromosomes in the GnomAD database, including 316 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 0.041 ( 316 hom., cov: 32)
Consequence
CWF19L2
NM_152434.3 intron
NM_152434.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0480
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=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CWF19L2 | NM_152434.3 | c.1617+5962A>G | intron_variant | ENST00000282251.10 | |||
CWF19L2 | XM_047426419.1 | c.189+5962A>G | intron_variant | ||||
CWF19L2 | XR_007062452.1 | n.1626+5962A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CWF19L2 | ENST00000282251.10 | c.1617+5962A>G | intron_variant | 1 | NM_152434.3 | P1 | |||
CWF19L2 | ENST00000431778.5 | c.1260+5962A>G | intron_variant, NMD_transcript_variant | 1 | |||||
CWF19L2 | ENST00000532251.1 | c.1260+5962A>G | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0406 AC: 6178AN: 152024Hom.: 317 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0406 AC: 6174AN: 152144Hom.: 316 Cov.: 32 AF XY: 0.0477 AC XY: 3549AN XY: 74344
GnomAD4 genome
?
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6174
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152144
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32
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3549
AN XY:
74344
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449
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at