Variant 2-97113864-A-G 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_001354587.1(ANKRD36):c.125A>G(p.His42Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000552 in 1,607,124 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00059 ( 6 hom., cov: 32)

Exomes 𝑓: 0.00055 ( 71 hom. )

Consequence

ANKRD36
NM_001354587.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.92

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=0.008392215).

BP6

Variant 2-97113864-A-G is Benign according to our data. Variant chr2-97113864-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2651158.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD36	NM_001354587.1 linkuse as main transcript	c.125A>G	p.His42Arg	missense_variant	1/76	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD36	ENST00000420699.9 linkuse as main transcript	c.125A>G	p.His42Arg	missense_variant	1/76	5	NM_001354587.1	ENSP00000391950	P1	A6QL64-1
ANKRD36	ENST00000452478.2 linkuse as main transcript	n.313A>G		non_coding_transcript_exon_variant	1/3	1
ANKRD36	ENST00000461153.7 linkuse as main transcript	c.125A>G	p.His42Arg	missense_variant	1/75	5		ENSP00000419530	P1	A6QL64-1
ANKRD36	ENST00000652721.1 linkuse as main transcript	c.125A>G	p.His42Arg	missense_variant	1/76			ENSP00000498611	P1	A6QL64-1

Frequencies

GnomAD3 genomes

AF:

0.000587

AC:

AN:

148304

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000643

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000202

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00707

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000977

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.000300

Gnomad OTH

AF:

0.000987

GnomAD3 exomes

AF:

0.000305

AC:

AN:

248910

Hom.:

AF XY:

0.000303

AC XY:

AN XY:

135202

show subpopulations

Gnomad AFR exome

AF:

0.000454

Gnomad AMR exome

AF:

0.000319

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000842

Gnomad SAS exome

AF:

0.000196

Gnomad FIN exome

AF:

0.0000464

Gnomad NFE exome

AF:

0.000274

Gnomad OTH exome

AF:

0.000826

GnomAD4 exome

AF:

0.000548

AC:

800

AN:

1458712

Hom.:

Cov.:

AF XY:

0.000562

AC XY:

408

AN XY:

725682

show subpopulations

Gnomad4 AFR exome

AF:

0.000692

Gnomad4 AMR exome

AF:

0.000471

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0134

Gnomad4 SAS exome

AF:

0.000128

Gnomad4 FIN exome

AF:

0.0000376

Gnomad4 NFE exome

AF:

0.000175

Gnomad4 OTH exome

AF:

0.000349

GnomAD4 genome

AF:

0.000586

AC:

AN:

148412

Hom.:

Cov.:

AF XY:

0.000663

AC XY:

AN XY:

72424

show subpopulations

Gnomad4 AFR

AF:

0.000641

Gnomad4 AMR

AF:

0.000202

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00708

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0000977

Gnomad4 NFE

AF:

0.000300

Gnomad4 OTH

AF:

0.000980

Alfa

AF:

0.000255

Hom.:

ExAC

AF:

0.000364

AC:

EpiCase

AF:

0.000491

EpiControl

AF:

0.000652

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

ANKRD36: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.75

CADD

Benign

0.15

DANN

Benign

0.20

DEOGEN2

Benign

0.0012

.;.;.;T

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.0099

LIST_S2

Benign

0.075

T;T;T;T

M_CAP

Benign

0.0020

MetaRNN

Benign

0.0084

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.010

.;.;.;N

MutationTaster

Benign

1.0

N;N

PrimateAI

Uncertain

0.63

PROVEAN

Benign

0.040

.;N;.;N

REVEL

Benign

0.051

Sift

Benign

0.40

.;T;.;T

Sift4G

Benign

0.34

.;T;T;T

Polyphen

0.0010

.;.;.;B

Vest4

0.087, 0.13, 0.072

MutPred

0.55

Gain of MoRF binding (P = 0.0065);Gain of MoRF binding (P = 0.0065);Gain of MoRF binding (P = 0.0065);Gain of MoRF binding (P = 0.0065);

MVP

0.20

ClinPred

0.0058

GERP RS

-1.9

Varity_R

0.024

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