Genetic Variant ANKRD11:c.*268G>A (chr16-89268210-C-T) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_013275.6(ANKRD11):c.*268G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 0 hom., cov: 11)

Exomes 𝑓: 0.0041 ( 4 hom. )

Failed GnomAD Quality Control

Consequence

ANKRD11
NM_013275.6 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.375

Variant links:

Genes affected

ANKRD11 (HGNC:21316): (ankyrin repeat domain containing 11) This locus encodes an ankryin repeat domain-containing protein. The encoded protein inhibits ligand-dependent activation of transcription. Mutations in this gene have been associated with KBG syndrome, which is characterized by macrodontia, distinctive craniofacial features, short stature, skeletal anomalies, global developmental delay, seizures and intellectual disability. Alternatively spliced transcript variants have been described. Related pseudogenes exist on chromosomes 2 and X. [provided by RefSeq, Jan 2012]

ANKRD11 links:

ENSG00000268218 (HGNC:):

ENSG00000268218 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 16-89268210-C-T is Benign according to our data. Variant chr16-89268210-C-T is described in ClinVar as [Benign]. Clinvar id is 1276986.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ANKRD11	NM_013275.6 link	c.*268G>A	3_prime_UTR_variant	Exon 13 of 13	ENST00000301030.10	NP_037407.4	Q6UB99
ANKRD11	NM_001256182.2 link	c.*268G>A	3_prime_UTR_variant	Exon 14 of 14		NP_001243111.1	Q6UB99
ANKRD11	NM_001256183.2 link	c.*268G>A	3_prime_UTR_variant	Exon 13 of 13		NP_001243112.1	Q6UB99

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD11	ENST00000301030 link	c.*268G>A		3_prime_UTR_variant	Exon 13 of 13	5	NM_013275.6	ENSP00000301030.4		Q6UB99

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

286

AN:

90620

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000737

Gnomad AMI

AF:

0.00489

Gnomad AMR

AF:

0.00310

Gnomad ASJ

AF:

0.00389

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00136

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00373

Gnomad NFE

AF:

0.00491

Gnomad OTH

AF:

0.00258

GnomAD3 exomes

AF:

0.00364

AC:

128

AN:

35200

Hom.:

AF XY:

0.00375

AC XY:

AN XY:

18390

show subpopulations

Gnomad AFR exome

AF:

0.000789

Gnomad AMR exome

AF:

0.00363

Gnomad ASJ exome

AF:

0.00668

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00343

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00542

Gnomad OTH exome

AF:

0.00485

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00407

AC:

585

AN:

143812

Hom.:

Cov.:

AF XY:

0.00417

AC XY:

317

AN XY:

76078

show subpopulations

Gnomad4 AFR exome

AF:

0.000628

Gnomad4 AMR exome

AF:

0.00345

Gnomad4 ASJ exome

AF:

0.00705

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00373

Gnomad4 FIN exome

AF:

0.000304

Gnomad4 NFE exome

AF:

0.00491

Gnomad4 OTH exome

AF:

0.00295

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00315

AC:

286

AN:

90686

Hom.:

Cov.:

AF XY:

0.00297

AC XY:

116

AN XY:

39118

show subpopulations

Gnomad4 AFR

AF:

0.000734

Gnomad4 AMR

AF:

0.00310

Gnomad4 ASJ

AF:

0.00389

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00136

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00491

Gnomad4 OTH

AF:

0.00255

Alfa

AF:

0.00288

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Apr 13, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

1.6

DANN

Benign

0.88

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