chr12-88505276-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_000899.5(KITLG):c.783-41T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000722 in 1,487,554 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00043 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00076 ( 8 hom. )
Consequence
KITLG
NM_000899.5 intron
NM_000899.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.583
Genes affected
KITLG (HGNC:6343): (KIT ligand) This gene encodes the ligand of the tyrosine-kinase receptor encoded by the KIT locus. This ligand is a pleiotropic factor that acts in utero in germ cell and neural cell development, and hematopoiesis, all believed to reflect a role in cell migration. In adults, it functions pleiotropically, while mostly noted for its continued requirement in hematopoiesis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 12-88505276-A-T is Benign according to our data. Variant chr12-88505276-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 1211693.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000427 (65/152300) while in subpopulation SAS AF= 0.00104 (5/4822). AF 95% confidence interval is 0.000482. There are 1 homozygotes in gnomad4. There are 28 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KITLG | NM_000899.5 | c.783-41T>A | intron_variant | ENST00000644744.1 | |||
KITLG | NM_003994.6 | c.699-41T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KITLG | ENST00000644744.1 | c.783-41T>A | intron_variant | NM_000899.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000434 AC: 66AN: 152182Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000943 AC: 231AN: 244990Hom.: 1 AF XY: 0.00117 AC XY: 155AN XY: 132432
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GnomAD4 exome AF: 0.000756 AC: 1009AN: 1335254Hom.: 8 Cov.: 21 AF XY: 0.000876 AC XY: 588AN XY: 671278
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GnomAD4 genome ? AF: 0.000427 AC: 65AN: 152300Hom.: 1 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74468
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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 | GeneDx | Jul 21, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at