rs4971088
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173852.4(KRTCAP2):c.224-550A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 150,220 control chromosomes in the GnomAD database, including 24,112 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 0.56 ( 24097 hom., cov: 28)
Exomes 𝑓: 0.43 ( 15 hom. )
Consequence
KRTCAP2
NM_173852.4 intron
NM_173852.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.906
Genes affected
KRTCAP2 (HGNC:28942): (keratinocyte associated protein 2) Enables enzyme activator activity. Involved in protein N-linked glycosylation via arginine. Is active in oligosaccharyltransferase complex. [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=-1.01).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTCAP2 | NM_173852.4 | c.224-550A>T | intron_variant | ENST00000295682.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTCAP2 | ENST00000295682.6 | c.224-550A>T | intron_variant | 1 | NM_173852.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.559 AC: 83820AN: 149994Hom.: 24052 Cov.: 28
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GnomAD4 exome AF: 0.426 AC: 52AN: 122Hom.: 15 Cov.: 0 AF XY: 0.443 AC XY: 31AN XY: 70
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GnomAD4 genome ? AF: 0.559 AC: 83911AN: 150098Hom.: 24097 Cov.: 28 AF XY: 0.560 AC XY: 40953AN XY: 73070
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ClinVar
Not reported inComputational scores
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Name
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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