Variant chr19-4207296-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001393985.1(ANKRD24):c.521T>C(p.Leu174Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00421 in 1,613,840 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0035 ( 2 hom., cov: 31)

Exomes 𝑓: 0.0043 ( 27 hom. )

Consequence

ANKRD24
NM_001393985.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.02

Variant links:

Genes affected

ANKRD24 (HGNC:29424): (ankyrin repeat domain 24)

ANKRD24 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009562194).

BP6

Variant 19-4207296-T-C is Benign according to our data. Variant chr19-4207296-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2649031.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD24	NM_001393985.1 linkuse as main transcript	c.521T>C	p.Leu174Pro	missense_variant	8/22	ENST00000318934.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD24	ENST00000318934.9 linkuse as main transcript	c.521T>C	p.Leu174Pro	missense_variant	8/22	5	NM_001393985.1	A2	Q8TF21-1

Frequencies

GnomAD3 genomes

AF:

0.00351

AC:

533

AN:

152046

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000652

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00197

Gnomad ASJ

AF:

0.00663

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00189

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00629

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00314

AC:

782

AN:

249230

Hom.:

AF XY:

0.00319

AC XY:

431

AN XY:

135210

show subpopulations

Gnomad AFR exome

AF:

0.000904

Gnomad AMR exome

AF:

0.000696

Gnomad ASJ exome

AF:

0.00686

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00223

Gnomad NFE exome

AF:

0.00536

Gnomad OTH exome

AF:

0.00347

GnomAD4 exome

AF:

0.00428

AC:

6259

AN:

1461676

Hom.:

Cov.:

AF XY:

0.00438

AC XY:

3185

AN XY:

727122

show subpopulations

Gnomad4 AFR exome

AF:

0.000627

Gnomad4 AMR exome

AF:

0.000715

Gnomad4 ASJ exome

AF:

0.00719

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00285

Gnomad4 NFE exome

AF:

0.00507

Gnomad4 OTH exome

AF:

0.00373

GnomAD4 genome

AF:

0.00350

AC:

533

AN:

152164

Hom.:

Cov.:

AF XY:

0.00325

AC XY:

242

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.000650

Gnomad4 AMR

AF:

0.00196

Gnomad4 ASJ

AF:

0.00663

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00189

Gnomad4 NFE

AF:

0.00629

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00572

Hom.:

Bravo

AF:

0.00295

TwinsUK

AF:

0.00324

AC:

ALSPAC

AF:

0.00727

AC:

ESP6500AA

AF:

0.000755

AC:

ESP6500EA

AF:

0.00420

AC:

ExAC

AF:

0.00337

AC:

408

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00474

EpiControl

AF:

0.00409

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

ANKRD24: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.25

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.21

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.023

T;T;T;.

Eigen

Benign

0.18

Eigen_PC

Uncertain

0.27

FATHMM_MKL

Uncertain

0.86

LIST_S2

Benign

0.66

.;T;T;T

M_CAP

Benign

0.034

MetaRNN

Benign

0.0096

T;T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.98

L;L;.;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.66

PROVEAN

Uncertain

-3.7

.;D;.;D

REVEL

Uncertain

0.34

Sift

Uncertain

0.017

.;D;.;D

Sift4G

Uncertain

0.042

D;D;T;D

Polyphen

1.0

D;D;.;B

Vest4

0.71

MVP

0.70

MPC

1.1

ClinPred

0.022

GERP RS

4.9

Varity_R

0.61

gMVP

0.56

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