rs3826549
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000526.5(KRT14):āc.369T>Cā(p.Asn123=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 1,613,754 control chromosomes in the GnomAD database, including 283,068 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.57 ( 25950 hom., cov: 31)
Exomes š: 0.59 ( 257118 hom. )
Consequence
KRT14
NM_000526.5 synonymous
NM_000526.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.276
Genes affected
KRT14 (HGNC:6416): (keratin 14) This gene encodes a member of the keratin family, the most diverse group of intermediate filaments. This gene product, a type I keratin, is usually found as a heterotetramer with two keratin 5 molecules, a type II keratin. Together they form the cytoskeleton of epithelial cells. Mutations in the genes for these keratins are associated with epidermolysis bullosa simplex. At least one pseudogene has been identified at 17p12-p11. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
?
Variant 17-41586466-A-G is Benign according to our data. Variant chr17-41586466-A-G is described in ClinVar as [Benign]. Clinvar id is 66346.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-41586466-A-G is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.276 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT14 | NM_000526.5 | c.369T>C | p.Asn123= | synonymous_variant | 1/8 | ENST00000167586.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT14 | ENST00000167586.7 | c.369T>C | p.Asn123= | synonymous_variant | 1/8 | 1 | NM_000526.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.575 AC: 87247AN: 151762Hom.: 25934 Cov.: 31
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GnomAD3 exomes AF: 0.644 AC: 161967AN: 251458Hom.: 54299 AF XY: 0.641 AC XY: 87143AN XY: 135910
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GnomAD4 exome AF: 0.586 AC: 857284AN: 1461874Hom.: 257118 Cov.: 93 AF XY: 0.590 AC XY: 428742AN XY: 727232
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GnomAD4 genome ? AF: 0.575 AC: 87307AN: 151880Hom.: 25950 Cov.: 31 AF XY: 0.584 AC XY: 43331AN XY: 74242
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ClinVar
Significance: Benign
Submissions summary: Benign:4Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2Other:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
not provided, no classification provided | literature only | Epithelial Biology; Institute of Medical Biology, Singapore | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Epidermolysis bullosa simplex 1A, generalized severe;C0080333:Epidermolysis bullosa simplex 1C, localized;C0343111:Naegeli-Franceschetti-Jadassohn syndrome;C0406778:Dermatopathia pigmentosa reticularis;C3715082:Epidermolysis bullosa simplex 1D, generalized, intermediate or severe, autosomal recessive;C5561924:Epidermolysis bullosa simplex, Koebner type Benign:1
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 11, 2021 | - - |
Computational scores
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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