rs7313402
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014653.4(WSCD2):c.498-928C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,920 control chromosomes in the GnomAD database, including 17,991 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 0.48 ( 17991 hom., cov: 32)
Consequence
WSCD2
NM_014653.4 intron
NM_014653.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.275
Genes affected
WSCD2 (HGNC:29117): (WSC domain containing 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.77).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WSCD2 | NM_014653.4 | c.498-928C>A | intron_variant | ENST00000547525.6 | |||
LOC124903077 | XR_007063583.1 | n.183-18174G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WSCD2 | ENST00000547525.6 | c.498-928C>A | intron_variant | 1 | NM_014653.4 | P1 | |||
WSCD2 | ENST00000332082.8 | c.498-928C>A | intron_variant | 1 | P1 | ||||
WSCD2 | ENST00000549903.1 | c.498-928C>A | intron_variant | 5 | |||||
WSCD2 | ENST00000551638.5 | c.39-928C>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.484 AC: 73428AN: 151804Hom.: 17972 Cov.: 32
GnomAD3 genomes
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151804
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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: 0.484 AC: 73488AN: 151920Hom.: 17991 Cov.: 32 AF XY: 0.489 AC XY: 36269AN XY: 74240
GnomAD4 genome
?
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AC:
73488
AN:
151920
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32
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36269
AN XY:
74240
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1976
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3478
ClinVar
Not reported inComputational scores
Source:
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