Genetic Variant ANKRD36:p.Gly4Asp (chr2-97113750-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The NM_001354587.1(ANKRD36):c.11G>A(p.Gly4Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,608,904 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0012 ( 28 hom. )

Consequence

ANKRD36
NM_001354587.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.09

Variant links:

Genes affected

ANKRD36 (HGNC:24079): (ankyrin repeat domain 36)

ANKRD36 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=0.0074519515).

BP6

Variant 2-97113750-G-A is Benign according to our data. Variant chr2-97113750-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2651156.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-97113750-G-A is described in Lovd as [Likely_benign].

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36	NM_001354587.1 link	c.11G>A	p.Gly4Asp	missense_variant	Exon 1 of 76	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ANKRD36	ENST00000420699.9 link	c.11G>A	p.Gly4Asp	missense_variant	Exon 1 of 76	5	NM_001354587.1	ENSP00000391950.4	A6QL64-1
ANKRD36	ENST00000452478.2 link	n.199G>A		non_coding_transcript_exon_variant	Exon 1 of 3	1
ANKRD36	ENST00000461153.7 link	c.11G>A	p.Gly4Asp	missense_variant	Exon 1 of 75	5		ENSP00000419530.3	A6QL64-1
ANKRD36	ENST00000652721.1 link	c.11G>A	p.Gly4Asp	missense_variant	Exon 1 of 76			ENSP00000498611.1	A6QL64-1

Frequencies

GnomAD3 genomes

AF:

0.00220

AC:

334

AN:

151752

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000579

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00315

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000598

Gnomad SAS

AF:

0.000841

Gnomad FIN

AF:

0.000854

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.00340

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.000687

AC:

170

AN:

247564

Hom.:

AF XY:

0.000669

AC XY:

AN XY:

134554

show subpopulations

Gnomad AFR exome

AF:

0.000130

Gnomad AMR exome

AF:

0.00105

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000197

Gnomad FIN exome

AF:

0.000186

Gnomad NFE exome

AF:

0.00105

Gnomad OTH exome

AF:

0.000667

GnomAD4 exome

AF:

0.00116

AC:

1689

AN:

1457048

Hom.:

Cov.:

AF XY:

0.00122

AC XY:

882

AN XY:

724768

show subpopulations

Gnomad4 AFR exome

AF:

0.000120

Gnomad4 AMR exome

AF:

0.00177

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.0000256

Gnomad4 SAS exome

AF:

0.000604

Gnomad4 FIN exome

AF:

0.000772

Gnomad4 NFE exome

AF:

0.00121

Gnomad4 OTH exome

AF:

0.00208

GnomAD4 genome

AF:

0.00220

AC:

334

AN:

151856

Hom.:

Cov.:

AF XY:

0.00208

AC XY:

154

AN XY:

74146

show subpopulations

Gnomad4 AFR

AF:

0.000577

Gnomad4 AMR

AF:

0.00315

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000599

Gnomad4 SAS

AF:

0.000841

Gnomad4 FIN

AF:

0.000854

Gnomad4 NFE

AF:

0.00340

Gnomad4 OTH

AF:

0.00430

Alfa

AF:

0.00141

Hom.:

Bravo

AF:

0.00260

ExAC

AF:

0.000323

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ANKRD36: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.10

DANN

Benign

0.76

DEOGEN2

Benign

0.0059

.;.;.;T

Eigen

Benign

-2.1

Eigen_PC

Benign

-2.2

FATHMM_MKL

Benign

0.014

LIST_S2

Benign

0.20

T;T;T;T

M_CAP

Benign

0.0012

MetaRNN

Benign

0.0075

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.34

.;.;.;N

PrimateAI

Uncertain

0.54

PROVEAN

Benign

-0.83

.;N;.;N

REVEL

Benign

0.017

Sift

Benign

0.96

.;T;.;T

Sift4G

Benign

0.87

.;T;T;T

Polyphen

0.0

.;.;.;B

Vest4

0.12, 0.18, 0.14

MVP

0.030

ClinPred

0.00092

GERP RS

-0.91

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.083

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