chr9-98745553-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173551.5(ANKS6):c.2511+6G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000041 in 1,608,310 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000040 ( 0 hom. )
Consequence
ANKS6
NM_173551.5 splice_donor_region, intron
NM_173551.5 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.001786
2
Clinical Significance
Conservation
PhyloP100: -0.509
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS6 | NM_173551.5 | c.2511+6G>A | splice_donor_region_variant, intron_variant | ENST00000353234.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS6 | ENST00000353234.5 | c.2511+6G>A | splice_donor_region_variant, intron_variant | 1 | NM_173551.5 | P1 | |||
ANKS6 | ENST00000375019.6 | c.1608+6G>A | splice_donor_region_variant, intron_variant | 5 | |||||
ANKS6 | ENST00000444472.5 | c.919+6G>A | splice_donor_region_variant, intron_variant | 2 | |||||
ANKS6 | ENST00000634393.1 | n.1646+6G>A | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152196Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000842 AC: 21AN: 249550Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135388
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GnomAD4 exome AF: 0.0000398 AC: 58AN: 1455996Hom.: 0 Cov.: 30 AF XY: 0.0000414 AC XY: 30AN XY: 724846
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GnomAD4 genome AF: 0.0000525 AC: 8AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74480
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 17, 2023 | The c.2511+6G>A intronic alteration consists of a G to A substitution nucleotides after coding exon 14 in the ANKS6 gene. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at