rs3794260
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014653.4(WSCD2):c.383-1792G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.017 in 152,214 control chromosomes in the GnomAD database, including 97 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 0.017 ( 97 hom., cov: 32)
Consequence
WSCD2
NM_014653.4 intron
NM_014653.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.773
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=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WSCD2 | NM_014653.4 | c.383-1792G>A | intron_variant | ENST00000547525.6 | |||
LOC124903077 | XR_007063583.1 | n.183-13478C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WSCD2 | ENST00000547525.6 | c.383-1792G>A | intron_variant | 1 | NM_014653.4 | P1 | |||
WSCD2 | ENST00000332082.8 | c.383-1792G>A | intron_variant | 1 | P1 | ||||
WSCD2 | ENST00000549903.1 | c.383-1792G>A | intron_variant | 5 | |||||
WSCD2 | ENST00000551638.5 | c.-77-1792G>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0170 AC: 2583AN: 152096Hom.: 94 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: 0.0170 AC: 2594AN: 152214Hom.: 97 Cov.: 32 AF XY: 0.0183 AC XY: 1363AN XY: 74416
GnomAD4 genome
?
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2594
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152214
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32
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1363
AN XY:
74416
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324
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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