Genetic Variant ANKRD36:p.Tyr1569Tyr (chr2-97245372-T-C) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001354587.1(ANKRD36):c.4707T>C(p.Tyr1569Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00254 in 1,569,460 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 1 hom., cov: 19)

Exomes 𝑓: 0.0026 ( 59 hom. )

Consequence

ANKRD36
NM_001354587.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.231

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 2-97245372-T-C is Benign according to our data. Variant chr2-97245372-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2651166.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.231 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 59 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36	NM_001354587.1 link	c.4707T>C	p.Tyr1569Tyr	synonymous_variant	Exon 71 of 76	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD36	ENST00000420699.9 link	c.4707T>C	p.Tyr1569Tyr	synonymous_variant	Exon 71 of 76	5	NM_001354587.1	ENSP00000391950.4		A6QL64-1

Frequencies

GnomAD3 genomes

AF:

0.00224

AC:

330

AN:

147510

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000440

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00139

Gnomad ASJ

AF:

0.000297

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00379

Gnomad FIN

AF:

0.00711

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00290

Gnomad OTH

AF:

0.00397

GnomAD3 exomes

AF:

0.00243

AC:

390

AN:

160824

Hom.:

AF XY:

0.00261

AC XY:

222

AN XY:

85014

show subpopulations

Gnomad AFR exome

AF:

0.000772

Gnomad AMR exome

AF:

0.000413

Gnomad ASJ exome

AF:

0.000232

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00458

Gnomad FIN exome

AF:

0.00546

Gnomad NFE exome

AF:

0.00255

Gnomad OTH exome

AF:

0.00312

GnomAD4 exome

AF:

0.00257

AC:

3652

AN:

1421856

Hom.:

Cov.:

AF XY:

0.00279

AC XY:

1965

AN XY:

703944

show subpopulations

Gnomad4 AFR exome

AF:

0.000604

Gnomad4 AMR exome

AF:

0.00114

Gnomad4 ASJ exome

AF:

0.0000392

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00593

Gnomad4 FIN exome

AF:

0.00573

Gnomad4 NFE exome

AF:

0.00245

Gnomad4 OTH exome

AF:

0.00217

GnomAD4 genome

AF:

0.00224

AC:

330

AN:

147604

Hom.:

Cov.:

AF XY:

0.00257

AC XY:

184

AN XY:

71612

show subpopulations

Gnomad4 AFR

AF:

0.000439

Gnomad4 AMR

AF:

0.00139

Gnomad4 ASJ

AF:

0.000297

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00380

Gnomad4 FIN

AF:

0.00711

Gnomad4 NFE

AF:

0.00290

Gnomad4 OTH

AF:

0.00395

Alfa

AF:

0.00340

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ANKRD36: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.3

DANN

Benign

0.23

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