Variant rs6855349 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_032217.5(ANKRD17):c.6609C>T(p.Leu2203=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 1,613,908 control chromosomes in the GnomAD database, including 141,813 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 10642 hom., cov: 32)

Exomes 𝑓: 0.42 ( 131171 hom. )

Consequence

ANKRD17
NM_032217.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.35

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP7

Synonymous conserved (PhyloP=1.35 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.438 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.6609C>T	p.Leu2203=	synonymous_variant	29/34	ENST00000358602.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD17	ENST00000358602.9 linkuse as main transcript	c.6609C>T	p.Leu2203=	synonymous_variant	29/34	5	NM_032217.5		O75179-1
ANKRD17	ENST00000509867.6 linkuse as main transcript	c.6270C>T	p.Leu2090=	synonymous_variant	29/34	1		P1	O75179-7
ANKRD17	ENST00000558247.5 linkuse as main transcript	c.6261C>T	p.Leu2087=	synonymous_variant	29/34	1
ANKRD17	ENST00000330838.10 linkuse as main transcript	c.5856C>T	p.Leu1952=	synonymous_variant	28/33	2			O75179-6

Frequencies

GnomAD3 genomes

AF:

0.368

AC:

55967

AN:

151936

Hom.:

10638

Cov.:

show subpopulations

Gnomad AFR

AF:

0.271

Gnomad AMI

AF:

0.440

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.373

Gnomad SAS

AF:

0.453

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.430

Gnomad OTH

AF:

0.350

GnomAD3 exomes

AF:

0.389

AC:

97790

AN:

251388

Hom.:

19874

AF XY:

0.400

AC XY:

54341

AN XY:

135862

show subpopulations

Gnomad AFR exome

AF:

0.269

Gnomad AMR exome

AF:

0.264

Gnomad ASJ exome

AF:

0.369

Gnomad EAS exome

AF:

0.384

Gnomad SAS exome

AF:

0.450

Gnomad FIN exome

AF:

0.396

Gnomad NFE exome

AF:

0.428

Gnomad OTH exome

AF:

0.407

GnomAD4 exome

AF:

0.420

AC:

614668

AN:

1461854

Hom.:

131171

Cov.:

AF XY:

0.422

AC XY:

307119

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.267

Gnomad4 AMR exome

AF:

0.268

Gnomad4 ASJ exome

AF:

0.375

Gnomad4 EAS exome

AF:

0.354

Gnomad4 SAS exome

AF:

0.455

Gnomad4 FIN exome

AF:

0.402

Gnomad4 NFE exome

AF:

0.434

Gnomad4 OTH exome

AF:

0.404

GnomAD4 genome

AF:

0.368

AC:

55997

AN:

152054

Hom.:

10642

Cov.:

AF XY:

0.365

AC XY:

27090

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.271

Gnomad4 AMR

AF:

0.312

Gnomad4 ASJ

AF:

0.373

Gnomad4 EAS

AF:

0.373

Gnomad4 SAS

AF:

0.454

Gnomad4 FIN

AF:

0.390

Gnomad4 NFE

AF:

0.430

Gnomad4 OTH

AF:

0.347

Alfa

AF:

0.411

Hom.:

21105

Bravo

AF:

0.355

Asia WGS

AF:

0.367

AC:

1276

AN:

3478

EpiCase

AF:

0.429

EpiControl

AF:

0.430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

4.5

DANN

Benign

0.72

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over