Variant rs758109052 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001278444.2(ANKLE1):c.1771_1774delTTGT(p.Leu591fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 902,542 control chromosomes in the GnomAD database, including 3,277 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.22 ( 1866 hom., cov: 0)

Exomes 𝑓: 0.17 ( 1411 hom. )

Consequence

ANKLE1
NM_001278444.2 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.273

Variant links:

Genes affected

ANKLE1 (HGNC:26812): (ankyrin repeat and LEM domain containing 1) Enables endonuclease activity. Involved in positive regulation of response to DNA damage stimulus and protein export from nucleus. Located in cytosol and nucleoplasm. Colocalizes with nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ANKLE1 links:

ANKLE1 (HGNC:):

ANKLE1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 19-17286688-GTGTT-G is Benign according to our data. Variant chr19-17286688-GTGTT-G is described in ClinVar as [Benign]. Clinvar id is 402369.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKLE1	NM_152363.6 linkuse as main transcript	c.140_143delTTGT		3_prime_UTR_variant	9/9	ENST00000404085.7	NP_689576.6	Q8NAG6-2A0A499FJM0B4E124

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKLE1	ENST00000404085.7 linkuse as main transcript	c.140_143delTTGT		3_prime_UTR_variant	9/9	2	NM_152363.6	ENSP00000384008.3		Q8NAG6-2

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

22635

AN:

100914

Hom.:

1860

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.0246

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.252

GnomAD3 exomes

AF:

0.134

AC:

8740

AN:

65312

Hom.:

160

AF XY:

0.132

AC XY:

4485

AN XY:

33936

show subpopulations

Gnomad AFR exome

AF:

0.147

Gnomad AMR exome

AF:

0.125

Gnomad ASJ exome

AF:

0.161

Gnomad EAS exome

AF:

0.0246

Gnomad SAS exome

AF:

0.104

Gnomad FIN exome

AF:

0.103

Gnomad NFE exome

AF:

0.176

Gnomad OTH exome

AF:

0.158

GnomAD4 exome

AF:

0.167

AC:

133631

AN:

801554

Hom.:

1411

AF XY:

0.170

AC XY:

65720

AN XY:

386214

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.164

Gnomad4 ASJ exome

AF:

0.262

Gnomad4 EAS exome

AF:

0.0307

Gnomad4 SAS exome

AF:

0.175

Gnomad4 FIN exome

AF:

0.273

Gnomad4 NFE exome

AF:

0.166

Gnomad4 OTH exome

AF:

0.184

GnomAD4 genome

AF:

0.224

AC:

22650

AN:

100988

Hom.:

1866

Cov.:

AF XY:

0.219

AC XY:

10750

AN XY:

49104

show subpopulations

Gnomad4 AFR

AF:

0.263

Gnomad4 AMR

AF:

0.194

Gnomad4 ASJ

AF:

0.294

Gnomad4 EAS

AF:

0.0247

Gnomad4 SAS

AF:

0.145

Gnomad4 FIN

AF:

0.146

Gnomad4 NFE

AF:

0.239

Gnomad4 OTH

AF:

0.253

Alfa

AF:

0.151

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Outside ROI, Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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