Variant chr4-73076961-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_032217.5(ANKRD17):c.7731G>A(p.Thr2577=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,610,202 control chromosomes in the GnomAD database, including 23,467 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (★).

Frequency

Genomes: 𝑓 0.13 ( 1772 hom., cov: 32)

Exomes 𝑓: 0.17 ( 21695 hom. )

Consequence

ANKRD17
NM_032217.5 synonymous

Scores

Clinical Significance

association criteria provided, single submitter O:1

Conservation

PhyloP100: 0.200

Variant links:

Genes affected

ANKRD17 (HGNC:23575): (ankyrin repeat domain 17) The protein encoded by this gene belongs to the family of ankyrin repeat-containing proteins, and contains two distinct arrays of ankyrin repeats in its amino-terminal region, one with 15 ankyrin repeats, and the other with 10 ankyrin repeats. It also contains a nuclear export signal, nuclear localization signal, and a cyclin-binding RXL motif. Localization of this protein to the nucleus has been shown experimentally, and interactions between this protein and cyclin-dependent kinase 2 have been observed. It has been suggested that this protein plays a role in both DNA replication and in both anti-viral and anti-bacterial innate immune pathways. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

ANKRD17 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BP7

Synonymous conserved (PhyloP=0.2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD17	NM_032217.5 linkuse as main transcript	c.7731G>A	p.Thr2577=	synonymous_variant	33/34	ENST00000358602.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD17	ENST00000358602.9 linkuse as main transcript	c.7731G>A	p.Thr2577=	synonymous_variant	33/34	5	NM_032217.5		O75179-1
ANKRD17	ENST00000509867.6 linkuse as main transcript	c.7392G>A	p.Thr2464=	synonymous_variant	33/34	1		P1	O75179-7
ANKRD17	ENST00000558247.5 linkuse as main transcript	c.7383G>A	p.Thr2461=	synonymous_variant	33/34	1
ANKRD17	ENST00000330838.10 linkuse as main transcript	c.6978G>A	p.Thr2326=	synonymous_variant	32/33	2			O75179-6

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20400

AN:

151988

Hom.:

1773

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0388

Gnomad AMI

AF:

0.250

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.224

Gnomad FIN

AF:

0.0946

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.160

GnomAD3 exomes

AF:

0.175

AC:

43323

AN:

247888

Hom.:

4289

AF XY:

0.176

AC XY:

23598

AN XY:

134012

show subpopulations

Gnomad AFR exome

AF:

0.0350

Gnomad AMR exome

AF:

0.242

Gnomad ASJ exome

AF:

0.172

Gnomad EAS exome

AF:

0.260

Gnomad SAS exome

AF:

0.225

Gnomad FIN exome

AF:

0.105

Gnomad NFE exome

AF:

0.162

Gnomad OTH exome

AF:

0.172

GnomAD4 exome

AF:

0.166

AC:

242336

AN:

1458096

Hom.:

21695

Cov.:

AF XY:

0.167

AC XY:

121226

AN XY:

725198

show subpopulations

Gnomad4 AFR exome

AF:

0.0337

Gnomad4 AMR exome

AF:

0.238

Gnomad4 ASJ exome

AF:

0.177

Gnomad4 EAS exome

AF:

0.287

Gnomad4 SAS exome

AF:

0.217

Gnomad4 FIN exome

AF:

0.101

Gnomad4 NFE exome

AF:

0.161

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.134

AC:

20395

AN:

152106

Hom.:

1772

Cov.:

AF XY:

0.134

AC XY:

9996

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.0387

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.181

Gnomad4 EAS

AF:

0.274

Gnomad4 SAS

AF:

0.224

Gnomad4 FIN

AF:

0.0946

Gnomad4 NFE

AF:

0.159

Gnomad4 OTH

AF:

0.159

Alfa

AF:

0.163

Hom.:

3504

Bravo

AF:

0.139

Asia WGS

AF:

0.266

AC:

928

AN:

3478

EpiCase

AF:

0.174

EpiControl

AF:

0.168

ClinVar

Significance: association

Submissions summary: Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Lip and oral cavity carcinoma

Other:1

association, criteria provided, single submitter

case-control

Department of Biological Science, Sunandan Divatia School of Science, NMIMS University

A significant association of rs2306058 (ANKRD17) CT (odds ratio [OR] 0.72; 95% confidence interval [CI] 0.56-0.93) indicated decreased risk to oral cancer. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

6.4

DANN

Benign

0.68

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over