chr1-35441087-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_024874.5(KIAA0319L):c.2922G>A(p.Thr974=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0015 in 1,614,146 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0065 ( 16 hom., cov: 32)
Exomes 𝑓: 0.00098 ( 17 hom. )
Consequence
KIAA0319L
NM_024874.5 synonymous
NM_024874.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -8.51
Genes affected
KIAA0319L (HGNC:30071): (KIAA0319 like) Predicted to act upstream of or within several processes, including flagellated sperm motility; proacrosomal vesicle fusion; and receptor-mediated endocytosis of virus by host cell. Located in Golgi apparatus; cytoplasmic vesicle; and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.76).
BP6
Variant 1-35441087-C-T is Benign according to our data. Variant chr1-35441087-C-T is described in ClinVar as [Benign]. Clinvar id is 786460.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-8.51 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00648 (986/152268) while in subpopulation AFR AF= 0.021 (872/41530). AF 95% confidence interval is 0.0198. There are 16 homozygotes in gnomad4. There are 451 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 16 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA0319L | NM_024874.5 | c.2922G>A | p.Thr974= | synonymous_variant | 20/21 | ENST00000325722.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0319L | ENST00000325722.8 | c.2922G>A | p.Thr974= | synonymous_variant | 20/21 | 1 | NM_024874.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00647 AC: 985AN: 152150Hom.: 16 Cov.: 32
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GnomAD3 exomes AF: 0.00203 AC: 510AN: 251426Hom.: 9 AF XY: 0.00166 AC XY: 225AN XY: 135892
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GnomAD4 exome AF: 0.000978 AC: 1430AN: 1461878Hom.: 17 Cov.: 30 AF XY: 0.000857 AC XY: 623AN XY: 727240
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GnomAD4 genome AF: 0.00648 AC: 986AN: 152268Hom.: 16 Cov.: 32 AF XY: 0.00606 AC XY: 451AN XY: 74464
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Aug 17, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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