rs7633162
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001040432.4(ZCWPW2):c.611-6363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,764 control chromosomes in the GnomAD database, including 13,157 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 0.41 ( 13157 hom., cov: 32)
Consequence
ZCWPW2
NM_001040432.4 intron
NM_001040432.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.176
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 (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZCWPW2 | NM_001040432.4 | c.611-6363G>A | intron_variant | ENST00000383768.7 | |||
ZCWPW2 | NM_001324169.2 | c.611-6363G>A | intron_variant | ||||
ZCWPW2 | NM_001324170.2 | c.493-6363G>A | intron_variant | ||||
ZCWPW2 | NR_136708.2 | n.989-6363G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZCWPW2 | ENST00000383768.7 | c.611-6363G>A | intron_variant | 1 | NM_001040432.4 | P1 | |||
ZCWPW2 | ENST00000419130.5 | c.264-6363G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.412 AC: 62435AN: 151646Hom.: 13140 Cov.: 32
GnomAD3 genomes
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62435
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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: 0.412 AC: 62490AN: 151764Hom.: 13157 Cov.: 32 AF XY: 0.412 AC XY: 30589AN XY: 74158
GnomAD4 genome
?
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AC:
62490
AN:
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32
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30589
AN XY:
74158
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1907
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3462
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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