Genetic Variant ANKRD36:p.Met1? (chr2-97113741-T-A) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PVS1_SupportingBP6_ModerateBS2

The NM_001354587.1(ANKRD36):c.2T>A(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 1,608,552 control chromosomes in the GnomAD database, including 28 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 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0011 ( 25 hom. )

Consequence

ANKRD36
NM_001354587.1 start_lost

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.85

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 Likely_benign. Variant got -5 ACMG points.

PVS1

Start lost variant, no pathogenic variants between lost start and next in-frame start position. Next in-frame start position is after 13 codons. Genomic position: 97113776. Lost 0.006 part of the original CDS.

BP6

Variant 2-97113741-T-A is Benign according to our data. Variant chr2-97113741-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2651155.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36	NM_001354587.1 link	c.2T>A	p.Met1?	start_lost	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.2T>A	p.Met1?	start_lost	Exon 1 of 76	5	NM_001354587.1	ENSP00000391950.4	A6QL64-1
ANKRD36	ENST00000452478.2 link	n.190T>A		non_coding_transcript_exon_variant	Exon 1 of 3	1
ANKRD36	ENST00000461153.7 link	c.2T>A	p.Met1?	start_lost	Exon 1 of 75	5		ENSP00000419530.3	A6QL64-1
ANKRD36	ENST00000652721.1 link	c.2T>A	p.Met1?	start_lost	Exon 1 of 76			ENSP00000498611.1	A6QL64-1

Frequencies

GnomAD3 genomes

AF:

0.00223

AC:

334

AN:

150020

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000604

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00297

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000200

Gnomad SAS

AF:

0.000841

Gnomad FIN

AF:

0.00123

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00345

Gnomad OTH

AF:

0.00434

GnomAD3 exomes

AF:

0.000666

AC:

163

AN:

244622

Hom.:

AF XY:

0.000631

AC XY:

AN XY:

133104

show subpopulations

Gnomad AFR exome

AF:

0.0000650

Gnomad AMR exome

AF:

0.000937

Gnomad ASJ exome

AF:

0.000100

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000164

Gnomad FIN exome

AF:

0.000995

Gnomad NFE exome

AF:

0.000901

Gnomad OTH exome

AF:

0.000672

GnomAD4 exome

AF:

0.00114

AC:

1662

AN:

1458430

Hom.:

Cov.:

AF XY:

0.00120

AC XY:

870

AN XY:

725426

show subpopulations

Gnomad4 AFR exome

AF:

0.0000896

Gnomad4 AMR exome

AF:

0.00160

Gnomad4 ASJ exome

AF:

0.000153

Gnomad4 EAS exome

AF:

0.0000256

Gnomad4 SAS exome

AF:

0.000570

Gnomad4 FIN exome

AF:

0.00109

Gnomad4 NFE exome

AF:

0.00118

Gnomad4 OTH exome

AF:

0.00206

GnomAD4 genome

AF:

0.00222

AC:

334

AN:

150122

Hom.:

Cov.:

AF XY:

0.00212

AC XY:

155

AN XY:

73112

show subpopulations

Gnomad4 AFR

AF:

0.000602

Gnomad4 AMR

AF:

0.00297

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000200

Gnomad4 SAS

AF:

0.000842

Gnomad4 FIN

AF:

0.00123

Gnomad4 NFE

AF:

0.00345

Gnomad4 OTH

AF:

0.00434

Alfa

AF:

0.00204

Hom.:

ExAC

AF:

0.000774

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

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.61

CADD

Benign

7.0

DANN

Benign

0.76

DEOGEN2

Benign

0.00086

.;.;.;T

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.036

LIST_S2

Uncertain

0.90

D;D;D;D

M_CAP

Benign

0.0011

MetaRNN

Benign

0.020

T;T;T;T

MetaSVM

Benign

-0.99

PROVEAN

Benign

0.12

.;N;.;N

REVEL

Benign

0.052

Sift

Uncertain

0.0010

.;D;.;D

Sift4G

Uncertain

0.0030

.;D;D;D

Polyphen

0.051

.;.;.;B

Vest4

0.23, 0.25, 0.22

MVP

0.23

ClinPred

0.0099

GERP RS

-0.91

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

Varity_R

0.44

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