chr19-50908309-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004917.5(KLK4):c.612+50G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00532 in 1,605,664 control chromosomes in the GnomAD database, including 386 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.028 ( 195 hom., cov: 32)
Exomes 𝑓: 0.0030 ( 191 hom. )
Consequence
KLK4
NM_004917.5 intron
NM_004917.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.119
Genes affected
KLK4 (HGNC:6365): (kallikrein related peptidase 4) Kallikreins are a subgroup of serine proteases having diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis and some have potential as novel cancer and other disease biomarkers. This gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. In some tissues its expression is hormonally regulated. The expression pattern of a similar mouse protein in murine developing teeth supports a role for the protein in the degradation of enamel proteins. Several transcript variants encoding different proteins have been found for this gene. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 19-50908309-C-T is Benign according to our data. Variant chr19-50908309-C-T is described in ClinVar as [Benign]. Clinvar id is 1245992.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0945 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLK4 | NM_004917.5 | c.612+50G>A | intron_variant | ENST00000324041.6 | NP_004908.4 | |||
KLK4 | NM_001302961.2 | c.327+50G>A | intron_variant | NP_001289890.1 | ||||
KLK4 | NR_126566.2 | n.601+50G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLK4 | ENST00000324041.6 | c.612+50G>A | intron_variant | 1 | NM_004917.5 | ENSP00000326159.1 |
Frequencies
GnomAD3 genomes AF: 0.0278 AC: 4224AN: 152108Hom.: 195 Cov.: 32
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GnomAD3 exomes AF: 0.00731 AC: 1800AN: 246274Hom.: 80 AF XY: 0.00565 AC XY: 754AN XY: 133458
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GnomAD4 exome AF: 0.00296 AC: 4300AN: 1453438Hom.: 191 Cov.: 32 AF XY: 0.00257 AC XY: 1860AN XY: 723280
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GnomAD4 genome AF: 0.0278 AC: 4237AN: 152226Hom.: 195 Cov.: 32 AF XY: 0.0270 AC XY: 2010AN XY: 74434
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 20, 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