rs3096299

chr16-89382255-G-Achr16-89382255-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013275.6(ANKRD11):c.-60+36029C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 151,754 control chromosomes in the GnomAD database, including 23,247 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.55 (23247 hom., cov: 30)
• Consequence: ANKRD11 NM_013275.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

Genes affected

LOC128462377 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC128462377	NM_001416403.1	c.9+36029C>T		intron_variant		ENST00000711617.1
ANKRD11	NM_013275.6	c.-60+36029C>T		intron_variant		ENST00000301030.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD11	ENST00000301030.10	c.-60+36029C>T		intron_variant		5	NM_013275.6	P1
	ENST00000711617.1	c.9+36029C>T		intron_variant			NM_001416403.1	A2

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83586 AN: 151638 Hom.: 23218 Cov.: 30

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.632

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.551 AC: 83663 AN: 151754 Hom.: 23247 Cov.: 30 AF XY: 0.548 AC XY: 40595 AN XY: 74108

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.634

Alfa AF: 0.579 Hom.: 43098

Bravo AF: 0.557

Asia WGS AF: 0.594 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.87
Dann	Benign	0.58
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs3096299; hg19: chr16-89448663;