chr9-98736320-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_173551.5(ANKS6):c.*199C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00227 in 1,411,292 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.012 ( 35 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 21 hom. )
Consequence
ANKS6
NM_173551.5 3_prime_UTR
NM_173551.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.82
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 9-98736320-G-A is Benign according to our data. Variant chr9-98736320-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1328662.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0117 (1778/152186) while in subpopulation AFR AF= 0.0412 (1710/41522). AF 95% confidence interval is 0.0396. There are 35 homozygotes in gnomad4. There are 817 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 35 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS6 | NM_173551.5 | c.*199C>T | 3_prime_UTR_variant | 15/15 | ENST00000353234.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS6 | ENST00000353234.5 | c.*199C>T | 3_prime_UTR_variant | 15/15 | 1 | NM_173551.5 | P1 | ||
ANKS6 | ENST00000375019.6 | c.1705+207C>T | intron_variant | 5 | |||||
ANKS6 | ENST00000444472.5 | c.*23+176C>T | intron_variant | 2 | |||||
ANKS6 | ENST00000634393.1 | n.1743+207C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0117 AC: 1779AN: 152068Hom.: 35 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1779
AN:
152068
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00113 AC: 1425AN: 1259106Hom.: 21 Cov.: 32 AF XY: 0.000995 AC XY: 605AN XY: 607760
GnomAD4 exome
AF:
AC:
1425
AN:
1259106
Hom.:
Cov.:
32
AF XY:
AC XY:
605
AN XY:
607760
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0117 AC: 1778AN: 152186Hom.: 35 Cov.: 32 AF XY: 0.0110 AC XY: 817AN XY: 74390
GnomAD4 genome
?
AF:
AC:
1778
AN:
152186
Hom.:
Cov.:
32
AF XY:
AC XY:
817
AN XY:
74390
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
5
AN:
3478
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 | May 19, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at