chr9-98736282-C-G

Position:

• chr9-98736282-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_173551.5(ANKS6):​c.*237G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 1,347,724 control chromosomes in the GnomAD database, including 335,108 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.64 (31622 hom., cov: 29)
  • Exomes 𝑓: 0.71 (303486 hom.)
• Consequence: ANKS6 NM_173551.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.214

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 9-98736282-C-G is Benign according to our data. Variant chr9-98736282-C-G is described in ClinVar as [Benign]. Clinvar id is 1279257.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKS6	NM_173551.5	c.*237G>C		3_prime_UTR_variant	15/15	ENST00000353234.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKS6	ENST00000353234.5	c.*237G>C		3_prime_UTR_variant	15/15	1	NM_173551.5	P1
ANKS6	ENST00000375019.6	c.1705+245G>C		intron_variant		5
ANKS6	ENST00000444472.5	c.*23+214G>C		intron_variant		2
ANKS6	ENST00000634393.1	n.1743+245G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96472 AN: 151518 Hom.: 31622 Cov.: 29

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.679

GnomAD4 exome AF: 0.707 AC: 846178 AN: 1196088 Hom.: 303486 Cov.: 43 AF XY: 0.706 AC XY: 404954 AN XY: 573616

Gnomad4 AFR exome AF: 0.504

Gnomad4 AMR exome AF: 0.592

Gnomad4 ASJ exome AF: 0.757

Gnomad4 EAS exome AF: 0.313

Gnomad4 SAS exome AF: 0.609

Gnomad4 FIN exome AF: 0.659

Gnomad4 NFE exome AF: 0.732

Gnomad4 OTH exome AF: 0.694

GnomAD4 genome AF: 0.636 AC: 96494 AN: 151636 Hom.: 31622 Cov.: 29 AF XY: 0.631 AC XY: 46740 AN XY: 74052

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.676

Alfa AF: 0.594 Hom.: 1978

Bravo AF: 0.625

Asia WGS AF: 0.472 AC: 1642 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.79
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1

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

LitVar

Other links and lift over

dbSNP: rs10760479; hg19: chr9-101498564;