3-108163651-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018010.4(IFT57):c.1111+12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000471 in 1,597,636 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0026 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00025 ( 2 hom. )
Consequence
IFT57
NM_018010.4 intron
NM_018010.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.844
Genes affected
IFT57 (HGNC:17367): (intraflagellar transport 57) Predicted to enable DNA binding activity. Acts upstream of or within activation of cysteine-type endopeptidase activity involved in apoptotic process; apoptotic process; and regulation of apoptotic process. Predicted to be located in ciliary basal body. Predicted to be part of axoneme and intraciliary transport particle B. Predicted to be active in Golgi apparatus; centrosome; and cilium. Implicated in orofaciodigital syndrome. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.82).
BP6
Variant 3-108163651-G-A is Benign according to our data. Variant chr3-108163651-G-A is described in ClinVar as [Benign]. Clinvar id is 1580303.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFT57 | NM_018010.4 | c.1111+12C>T | intron_variant | ENST00000264538.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFT57 | ENST00000264538.4 | c.1111+12C>T | intron_variant | 1 | NM_018010.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00257 AC: 391AN: 152058Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000735 AC: 184AN: 250238Hom.: 1 AF XY: 0.000591 AC XY: 80AN XY: 135270
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GnomAD4 exome AF: 0.000249 AC: 360AN: 1445462Hom.: 2 Cov.: 28 AF XY: 0.000194 AC XY: 140AN XY: 719914
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GnomAD4 genome AF: 0.00258 AC: 392AN: 152174Hom.: 1 Cov.: 32 AF XY: 0.00223 AC XY: 166AN XY: 74400
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 22, 2023 | - - |
Computational scores
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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