Variant 9-33534475-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001393611.1(ANKRD18B):c.708C>T(p.Ala236Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000626 in 1,548,846 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00061 ( 1 hom., cov: 31)

Exomes 𝑓: 0.00063 ( 6 hom. )

Consequence

ANKRD18B
NM_001393611.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.507

Variant links:

Genes affected

ANKRD18B (HGNC:23644): (ankyrin repeat domain 18B)

ANKRD18B links:

ANKRD18B (HGNC:):

ANKRD18B 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=-0.85).

BP6

Variant 9-33534475-C-T is Benign according to our data. Variant chr9-33534475-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2659149.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.507 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD18B	NM_001393611.1 linkuse as main transcript	c.708C>T	p.Ala236Ala	synonymous_variant	5/19	ENST00000684830.1	NP_001380540.1
ANKRD18B	NM_001353432.2 linkuse as main transcript	c.708C>T	p.Ala236Ala	synonymous_variant	5/20		NP_001340361.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ANKRD18B	ENST00000684830.1 linkuse as main transcript	c.708C>T	p.Ala236Ala	synonymous_variant	5/19		NM_001393611.1	ENSP00000510683.1	A0A8I5KZ96
ANKRD18B	ENST00000290943.10 linkuse as main transcript	c.708C>T	p.Ala236Ala	synonymous_variant	5/16	5		ENSP00000290943.6	A2A2Z9
ANKRD18B	ENST00000474881.6 linkuse as main transcript	n.210C>T		non_coding_transcript_exon_variant	2/4	3

Frequencies

GnomAD3 genomes

AF:

0.000612

AC:

AN:

152004

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000967

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.0225

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000147

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00148

AC:

231

AN:

155608

Hom.:

AF XY:

0.00138

AC XY:

113

AN XY:

82180

show subpopulations

Gnomad AFR exome

AF:

0.000124

Gnomad AMR exome

AF:

0.000166

Gnomad ASJ exome

AF:

0.0230

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000910

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000347

Gnomad OTH exome

AF:

0.00205

GnomAD4 exome

AF:

0.000628

AC:

877

AN:

1396842

Hom.:

Cov.:

AF XY:

0.000639

AC XY:

440

AN XY:

688844

show subpopulations

Gnomad4 AFR exome

AF:

0.000127

Gnomad4 AMR exome

AF:

0.000143

Gnomad4 ASJ exome

AF:

0.0239

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.0000638

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000131

Gnomad4 OTH exome

AF:

0.00207

GnomAD4 genome

AF:

0.000612

AC:

AN:

152004

Hom.:

Cov.:

AF XY:

0.000687

AC XY:

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.0000967

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.0225

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000147

Gnomad4 OTH

AF:

0.000478

Alfa

AF:

0.00215

Hom.:

Bravo

AF:

0.000604

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

Apr 01, 2022

ANKRD18B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.1

DANN

Benign

0.26

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