chr10-125980324-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_145235.5(FANK1):c.177T>C(p.Tyr59=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00131 in 1,613,958 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0066 ( 16 hom., cov: 32)
Exomes 𝑓: 0.00076 ( 10 hom. )
Consequence
FANK1
NM_145235.5 synonymous
NM_145235.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.689
Genes affected
FANK1 (HGNC:23527): (fibronectin type III and ankyrin repeat domains 1) Involved in regulation of apoptotic process and regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. Colocalizes with chromatin. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
Variant 10-125980324-T-C is Benign according to our data. Variant chr10-125980324-T-C is described in ClinVar as [Benign]. Clinvar id is 780916.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00656 (999/152316) while in subpopulation AFR AF= 0.0226 (940/41562). AF 95% confidence interval is 0.0214. There are 16 homozygotes in gnomad4. There are 479 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANK1 | NM_145235.5 | c.177T>C | p.Tyr59= | synonymous_variant | 2/11 | ENST00000368693.6 | |
FANK1 | NM_001350939.2 | c.177T>C | p.Tyr59= | synonymous_variant | 2/12 | ||
FANK1 | NM_001363549.2 | c.159T>C | p.Tyr53= | synonymous_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANK1 | ENST00000368693.6 | c.177T>C | p.Tyr59= | synonymous_variant | 2/11 | 1 | NM_145235.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00652 AC: 993AN: 152198Hom.: 15 Cov.: 32
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GnomAD3 exomes AF: 0.00180 AC: 451AN: 250972Hom.: 4 AF XY: 0.00129 AC XY: 175AN XY: 135658
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GnomAD4 exome AF: 0.000764 AC: 1117AN: 1461642Hom.: 10 Cov.: 31 AF XY: 0.000656 AC XY: 477AN XY: 727118
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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 | Invitae | Jan 08, 2018 | - - |
Computational scores
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Benign
Cadd
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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