chr9-98745398-AC-A

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

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.415
Variant links:
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
ANKS6NM_173551.5 linkuse as main transcriptc.2511+160del intron_variant ENST00000353234.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANKS6ENST00000353234.5 linkuse as main transcriptc.2511+160del intron_variant 1 NM_173551.5 P1Q68DC2-1
ANKS6ENST00000375019.6 linkuse as main transcriptc.1608+160del intron_variant 5
ANKS6ENST00000444472.5 linkuse as main transcriptc.919+160del intron_variant 2
ANKS6ENST00000634393.1 linkuse as main transcriptn.1646+160del intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.00521
AC:
792
AN:
152132
Hom.:
6
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0179
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00203
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.00430
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00523
AC:
797
AN:
152250
Hom.:
7
Cov.:
32
AF XY:
0.00523
AC XY:
389
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0180
Gnomad4 AMR
AF:
0.00203
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000588
Gnomad4 OTH
AF:
0.00426
Alfa
AF:
0.00413
Hom.:
0
Bravo
AF:
0.00620
Asia WGS
AF:
0.00173
AC:
6
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 submitterclinical testingGeneDxApr 09, 2021See Variant Classification Assertion Criteria. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs535407349; hg19: chr9-101507680; API