Variant 5-56111622-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_024669.3(ANKRD55):c.1126T>C(p.Ser376Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00674 in 1,579,604 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0046 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0070 ( 63 hom. )

Consequence

ANKRD55
NM_024669.3 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 5.95

Variant links:

Genes affected

ANKRD55 (HGNC:25681): (ankyrin repeat domain 55)

ANKRD55 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0075847805).

BP6

Variant 5-56111622-A-G is Benign according to our data. Variant chr5-56111622-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 719615.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD55	NM_024669.3 linkuse as main transcript	c.1126T>C	p.Ser376Pro	missense_variant	10/12	ENST00000341048.9
ANKRD55	XM_047417710.1 linkuse as main transcript	c.640T>C	p.Ser214Pro	missense_variant	6/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD55	ENST00000341048.9 linkuse as main transcript	c.1126T>C	p.Ser376Pro	missense_variant	10/12	2	NM_024669.3	P1	Q3KP44-1
ANKRD55	ENST00000434982.2 linkuse as main transcript	c.262T>C	p.Ser88Pro	missense_variant	2/4	1			Q3KP44-2
ANKRD55	ENST00000504958.6 linkuse as main transcript	c.997T>C	p.Ser333Pro	missense_variant	8/10	5
ANKRD55	ENST00000505970.2 linkuse as main transcript	n.809T>C		non_coding_transcript_exon_variant	7/7	3

Frequencies

GnomAD3 genomes

AF:

0.00462

AC:

702

AN:

152096

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00128

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00177

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00482

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00814

Gnomad OTH

AF:

0.00336

GnomAD3 exomes

AF:

0.00438

AC:

945

AN:

215648

Hom.:

AF XY:

0.00458

AC XY:

525

AN XY:

114750

show subpopulations

Gnomad AFR exome

AF:

0.00133

Gnomad AMR exome

AF:

0.000876

Gnomad ASJ exome

AF:

0.00161

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00146

Gnomad FIN exome

AF:

0.00778

Gnomad NFE exome

AF:

0.00683

Gnomad OTH exome

AF:

0.00431

GnomAD4 exome

AF:

0.00697

AC:

9948

AN:

1427390

Hom.:

Cov.:

AF XY:

0.00685

AC XY:

4843

AN XY:

707386

show subpopulations

Gnomad4 AFR exome

AF:

0.00109

Gnomad4 AMR exome

AF:

0.000881

Gnomad4 ASJ exome

AF:

0.00162

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00156

Gnomad4 FIN exome

AF:

0.00726

Gnomad4 NFE exome

AF:

0.00818

Gnomad4 OTH exome

AF:

0.00606

GnomAD4 genome

AF:

0.00461

AC:

702

AN:

152214

Hom.:

Cov.:

AF XY:

0.00430

AC XY:

320

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.00128

Gnomad4 AMR

AF:

0.00177

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00482

Gnomad4 NFE

AF:

0.00815

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00702

Hom.:

Bravo

AF:

0.00414

TwinsUK

AF:

0.00809

AC:

ALSPAC

AF:

0.00908

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00837

AC:

ExAC

AF:

0.00413

AC:

501

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2024	ANKRD55: BP4, BS2 -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Benign

-0.10

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.030

T;T;.

Eigen

Uncertain

0.46

Eigen_PC

Uncertain

0.48

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.86

D;T;T

M_CAP

Benign

0.033

MetaRNN

Benign

0.0076

T;T;T

MetaSVM

Benign

-0.81

MutationAssessor

Uncertain

2.3

M;.;.

MutationTaster

Benign

1.0

D;D;D;D

PrimateAI

Benign

0.39

PROVEAN

Benign

-1.4

N;N;D

REVEL

Benign

0.17

Sift

Uncertain

0.0020

D;D;D

Sift4G

Uncertain

0.024

D;D;D

Vest4

0.21

MVP

0.58

MPC

0.27

ClinPred

0.033

GERP RS

5.5

Varity_R

0.58

gMVP

0.58

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