rs1990624
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_033119.5(NKD1):c.*9284C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,140 control chromosomes in the GnomAD database, including 27,827 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 0.59 ( 27803 hom., cov: 32)
Exomes 𝑓: 0.74 ( 24 hom. )
Consequence
NKD1
NM_033119.5 3_prime_UTR
NM_033119.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.237
Genes affected
NKD1 (HGNC:17045): (NKD inhibitor of WNT signaling pathway 1) In the mouse, Nkd is a Dishevelled (see DVL1; MIM 601365)-binding protein that functions as a negative regulator of the Wnt (see WNT1; MIM 164820)-beta-catenin (see MIM 116806)-Tcf (see MIM 602272) signaling pathway.[supplied by OMIM, Jun 2003]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKD1 | NM_033119.5 | c.*9284C>A | 3_prime_UTR_variant | 10/10 | ENST00000268459.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKD1 | ENST00000268459.6 | c.*9284C>A | 3_prime_UTR_variant | 10/10 | 1 | NM_033119.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.595 AC: 90425AN: 151938Hom.: 27800 Cov.: 32
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GnomAD4 exome AF: 0.744 AC: 64AN: 86Hom.: 24 Cov.: 0 AF XY: 0.773 AC XY: 51AN XY: 66
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GnomAD4 genome ? AF: 0.595 AC: 90455AN: 152054Hom.: 27803 Cov.: 32 AF XY: 0.596 AC XY: 44297AN XY: 74324
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ClinVar
Not reported inComputational scores
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at