17-41084428-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_033061.4(KRTAP4-7):c.222C>T(p.Cys74=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00483 in 1,419,176 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0025 ( 0 hom., cov: 28)
Exomes 𝑓: 0.0051 ( 24 hom. )
Consequence
KRTAP4-7
NM_033061.4 synonymous
NM_033061.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.31
Genes affected
KRTAP4-7 (HGNC:18898): (keratin associated protein 4-7) This protein is a member of the keratin-associated protein (KAP) family. The KAP proteins form a matrix of keratin intermediate filaments which contribute to the structure of hair fibers. KAP family members appear to have unique, family-specific amino- and carboxyl-terminal regions and are subdivided into three multi-gene families according to amino acid composition: the high sulfur, the ultrahigh sulfur, and the high tyrosine/glycine KAPs. This protein is a member of the ultrahigh sulfur KAP family and the gene is localized to a cluster of KAPs at 17q12-q21. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 17-41084428-C-T is Benign according to our data. Variant chr17-41084428-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3341590.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.31 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 24 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRTAP4-7 | NM_033061.4 | c.222C>T | p.Cys74= | synonymous_variant | 1/1 | ENST00000391417.6 | NP_149050.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRTAP4-7 | ENST00000391417.6 | c.222C>T | p.Cys74= | synonymous_variant | 1/1 | NM_033061.4 | ENSP00000375236 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00254 AC: 383AN: 150832Hom.: 0 Cov.: 28
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GnomAD3 exomes AF: 0.00269 AC: 671AN: 249238Hom.: 1 AF XY: 0.00264 AC XY: 357AN XY: 135474
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GnomAD4 exome AF: 0.00510 AC: 6469AN: 1268234Hom.: 24 Cov.: 141 AF XY: 0.00501 AC XY: 3160AN XY: 630338
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GnomAD4 genome AF: 0.00254 AC: 384AN: 150942Hom.: 0 Cov.: 28 AF XY: 0.00224 AC XY: 165AN XY: 73816
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2024 | KRTAP4-7: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
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DANN
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Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 12
Find out detailed SpliceAI scores and Pangolin per-transcript scores at