9-98796327-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_173551.5(ANKS6):c.165C>T(p.Ala55Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 1,209,356 control chromosomes in the GnomAD database, including 66,736 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6599 hom., cov: 33)

Exomes 𝑓: 0.33 ( 60137 hom. )

Consequence

ANKS6
NM_173551.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.419

Publications

6 publications found

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]

ANKS6 Gene-Disease associations (from GenCC):

nephronophthisis 16
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
nephronophthisis 1
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
nephronophthisis 2
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ANKS6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 9-98796327-G-A is Benign according to our data. Variant chr9-98796327-G-A is described in ClinVar as [Benign]. Clinvar id is 262843.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.419 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKS6	NM_173551.5 link	c.165C>T	p.Ala55Ala	synonymous_variant	Exon 1 of 15	ENST00000353234.5	NP_775822.3	Q68DC2-1B3KXP1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ANKS6	ENST00000353234.5 link	c.165C>T	p.Ala55Ala	synonymous_variant	Exon 1 of 15	1	NM_173551.5	ENSP00000297837.6	Q68DC2-1
ANKS6	ENST00000471846.1 link	n.213C>T		non_coding_transcript_exon_variant	Exon 1 of 2	2
ANKS6	ENST00000375019.6 link	c.-42+357C>T		intron_variant	Intron 1 of 14	5		ENSP00000364159.2	A0A0A0MRS7

Frequencies

GnomAD3 genomes

AF:

0.283

AC:

42190

AN:

149218

Hom.:

6594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.288

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.358

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.401

Gnomad MID

AF:

0.312

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.287

GnomAD2 exomes

AF:

0.438

AC:

402

AN:

918

AF XY:

0.438

show subpopulations

Gnomad AFR exome

AF:

0.375

Gnomad AMR exome

AF:

0.471

Gnomad ASJ exome

AF:

0.391

Gnomad EAS exome

AF:

0.500

Gnomad FIN exome

AF:

0.574

Gnomad NFE exome

AF:

0.402

Gnomad OTH exome

AF:

0.433

GnomAD4 exome

AF:

0.333

AC:

353431

AN:

1060030

Hom.:

60137

Cov.:

AF XY:

0.335

AC XY:

168219

AN XY:

502518

show subpopulations

African (AFR)

AF:

0.125

AC:

2706

AN:

21696

American (AMR)

AF:

0.316

AC:

2389

AN:

7550

Ashkenazi Jewish (ASJ)

AF:

0.291

AC:

3774

AN:

12954

East Asian (EAS)

AF:

0.436

AC:

10580

AN:

24242

South Asian (SAS)

AF:

0.332

AC:

6861

AN:

20652

European-Finnish (FIN)

AF:

0.399

AC:

8265

AN:

20690

Middle Eastern (MID)

AF:

0.318

AC:

878

AN:

2762

European-Non Finnish (NFE)

AF:

0.336

AC:

304918

AN:

907840

Other (OTH)

AF:

0.314

AC:

13060

AN:

41644

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

12667

25334

38002

50669

63336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.283

AC:

42202

AN:

149326

Hom.:

6599

Cov.:

AF XY:

0.286

AC XY:

20857

AN XY:

72826

show subpopulations

African (AFR)

AF:

0.137

AC:

5641

AN:

41190

American (AMR)

AF:

0.289

AC:

4333

AN:

15010

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

1015

AN:

3426

East Asian (EAS)

AF:

0.359

AC:

1844

AN:

5142

South Asian (SAS)

AF:

0.351

AC:

1695

AN:

4826

European-Finnish (FIN)

AF:

0.401

AC:

3803

AN:

9480

Middle Eastern (MID)

AF:

0.308

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.341

AC:

22872

AN:

66982

Other (OTH)

AF:

0.288

AC:

597

AN:

2070

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1584

3168

4753

6337

7921

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.203

Hom.:

505

Bravo

AF:

0.270

Asia WGS

AF:

0.369

AC:

1201

AN:

3264

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Nov 10, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Nephronophthisis 16

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

ANKS6-related disorder

Benign:1

Sep 26, 2022

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

(source)

DANN

Benign

0.93

PhyloP100

0.42

PromoterAI

0.041

Neutral

(source)

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

2.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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9-98796327-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over