chr9-98745398-AC-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_173551.5(ANKS6):c.2511+160del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00523 in 152,250 control chromosomes in the GnomAD database, including 7 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0052 ( 7 hom., cov: 32)
Consequence
ANKS6
NM_173551.5 intron
NM_173551.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.415
Genes affected
ANKS6 (HGNC:26724): (ankyrin repeat and sterile alpha motif domain containing 6) This gene encodes a protein containing multiple ankyrin repeats and a SAM domain. It is thought that this protein may localize to the proximal region of the primary cilium, and may play a role in renal and cardiovascular development. Mutations in this gene have been shown to cause a form of nephronophthisis (NPHP16), a chronic tubulo-interstitial nephritis. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 9-98745398-AC-A is Benign according to our data. Variant chr9-98745398-AC-A is described in ClinVar as [Likely_benign]. Clinvar id is 1695470.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00523 (797/152250) while in subpopulation AFR AF= 0.018 (747/41556). AF 95% confidence interval is 0.0169. There are 7 homozygotes in gnomad4. There are 389 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS6 | NM_173551.5 | c.2511+160del | intron_variant | ENST00000353234.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS6 | ENST00000353234.5 | c.2511+160del | intron_variant | 1 | NM_173551.5 | P1 | |||
ANKS6 | ENST00000375019.6 | c.1608+160del | intron_variant | 5 | |||||
ANKS6 | ENST00000444472.5 | c.919+160del | intron_variant | 2 | |||||
ANKS6 | ENST00000634393.1 | n.1646+160del | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00521 AC: 792AN: 152132Hom.: 6 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00523 AC: 797AN: 152250Hom.: 7 Cov.: 32 AF XY: 0.00523 AC XY: 389AN XY: 74446
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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 | Apr 09, 2021 | See Variant Classification Assertion Criteria. - |
Computational scores
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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