Variant 2-97213610-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001354587.1(ANKRD36):c.3567A>G(p.Gly1189Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000849 in 138,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00085 ( 0 hom., cov: 21)

Exomes 𝑓: 0.00069 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ANKRD36
NM_001354587.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.780

Variant links:

Genes affected

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

ANKRD36 links:

ANKRD36 (HGNC:):

ANKRD36 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.11).

BP6

Variant 2-97213610-A-G is Benign according to our data. Variant chr2-97213610-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2651164.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.78 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD36	NM_001354587.1 linkuse as main transcript	c.3567A>G	p.Gly1189Gly	synonymous_variant	60/76	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ANKRD36	ENST00000420699.9 linkuse as main transcript	c.3567A>G	p.Gly1189Gly	synonymous_variant	60/76	5	NM_001354587.1	ENSP00000391950.4	A6QL64-1
ANKRD36	ENST00000461153.7 linkuse as main transcript	c.3567A>G	p.Gly1189Gly	synonymous_variant	60/75	5		ENSP00000419530.3	A6QL64-1
ANKRD36	ENST00000652721.1 linkuse as main transcript	c.3567A>G	p.Gly1189Gly	synonymous_variant	60/76			ENSP00000498611.1	A6QL64-1
ANKRD36	ENST00000421946.2 linkuse as main transcript	n.790A>G		non_coding_transcript_exon_variant	2/14	2

Frequencies

GnomAD3 genomes

AF:

0.000850

AC:

118

AN:

138868

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000138

Gnomad AMI

AF:

0.00893

Gnomad AMR

AF:

0.00150

Gnomad ASJ

AF:

0.000309

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00127

Gnomad OTH

AF:

0.000545

GnomAD3 exomes

AF:

0.000650

AC:

AN:

63106

Hom.:

AF XY:

0.000535

AC XY:

AN XY:

31776

show subpopulations

Gnomad AFR exome

AF:

0.000177

Gnomad AMR exome

AF:

0.000657

Gnomad ASJ exome

AF:

0.000520

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00118

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000693

AC:

300

AN:

432734

Hom.:

Cov.:

AF XY:

0.000668

AC XY:

153

AN XY:

228988

show subpopulations

Gnomad4 AFR exome

AF:

0.000263

Gnomad4 AMR exome

AF:

0.000520

Gnomad4 ASJ exome

AF:

0.000778

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000941

Gnomad4 OTH exome

AF:

0.00102

GnomAD4 genome

AF:

0.000849

AC:

118

AN:

138976

Hom.:

Cov.:

AF XY:

0.000867

AC XY:

AN XY:

66872

show subpopulations

Gnomad4 AFR

AF:

0.000137

Gnomad4 AMR

AF:

0.00150

Gnomad4 ASJ

AF:

0.000309

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00127

Gnomad4 OTH

AF:

0.000540

Alfa

AF:

0.000679

Hom.:

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

Dec 01, 2022

ANKRD36: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

1.1

DANN

Benign

0.077

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