rs713431
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001389244.1(KRT40):c.687+514C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,184 control chromosomes in the GnomAD database, including 1,395 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 0.13 ( 1395 hom., cov: 32)
Consequence
KRT40
NM_001389244.1 intron
NM_001389244.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.97
Genes affected
KRT40 (HGNC:26707): (keratin 40) This gene encodes a member of the type I (acidic) keratin family, which belongs to the superfamily of intermediate filament (IF) proteins. Keratins are heteropolymeric structural proteins which form the intermediate filament. These filaments, along with actin microfilaments and microtubules, compose the cytoskeleton of epithelial cells. The type I keratin genes are clustered in a region of chromosome 17q12-q21. [provided by RefSeq, Jul 2009]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT40 | NM_001389244.1 | c.687+514C>T | intron_variant | ENST00000377755.9 | |||
LOC107985072 | XR_001752886.2 | n.348-535G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT40 | ENST00000377755.9 | c.687+514C>T | intron_variant | 1 | NM_001389244.1 | P1 | |||
KRT40 | ENST00000398486.2 | c.687+514C>T | intron_variant | 1 | P1 | ||||
KRT40 | ENST00000684280.1 | c.687+514C>T | intron_variant | P1 | |||||
KRT40 | ENST00000461923.5 | c.688-469C>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.131 AC: 19981AN: 152066Hom.: 1396 Cov.: 32
GnomAD3 genomes
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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: 0.131 AC: 19991AN: 152184Hom.: 1395 Cov.: 32 AF XY: 0.134 AC XY: 9973AN XY: 74408
GnomAD4 genome
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19991
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32
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9973
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74408
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612
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3478
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