rs1173080093

Variant names:

• chr16-89268213-G-C
• rs1173080093
• NM_013275.6:c.*265C>G

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_013275.6(ANKRD11):​c.*265C>G 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 0.0029 (0 hom., cov: 11)
  • Exomes 𝑓: 0.0039 (4 hom.)
  • Failed GnomAD Quality Control
• Consequence: ANKRD11 NM_013275.6 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0470
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• KBG syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Illumina, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, G2P
• congenital heart defects, multiple types

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000268218 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 16-89268213-G-C is Benign according to our data. Variant chr16-89268213-G-C is described in ClinVar as Benign. ClinVar VariationId is 1222539.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013275.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD11	NM_013275.6	MANE Select	c.*265C>G		3_prime_UTR	Exon 13 of 13	NP_037407.4
	ANKRD11	NM_001256182.2		c.*265C>G		3_prime_UTR	Exon 14 of 14	NP_001243111.1	Q6UB99
	ANKRD11	NM_001256183.2		c.*265C>G		3_prime_UTR	Exon 13 of 13	NP_001243112.1	Q6UB99

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD11	ENST00000301030.10	TSL:5 MANE Select	c.*265C>G		3_prime_UTR	Exon 13 of 13	ENSP00000301030.4	Q6UB99
	ANKRD11	ENST00000378330.7	TSL:1	c.*265C>G		3_prime_UTR	Exon 14 of 14	ENSP00000367581.2	Q6UB99
	ANKRD11	ENST00000642600.2		c.*265C>G		3_prime_UTR	Exon 13 of 13	ENSP00000495226.1	Q6UB99

Frequencies

GnomAD3 genomes AF: 0.00291 AC: 262 AN: 90026 Hom.: 0 Cov.: 11

Gnomad AFR AF: 0.000836

Gnomad AMI AF: 0.00490

Gnomad AMR AF: 0.00298

Gnomad ASJ AF: 0.00392

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000918

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00376

Gnomad NFE AF: 0.00444

Gnomad OTH AF: 0.00172

GnomAD2 exomes AF: 0.00334 AC: 122 AN: 36534 AF XY: 0.00346

Gnomad AFR exome AF: 0.000504

Gnomad AMR exome AF: 0.00346

Gnomad ASJ exome AF: 0.00640

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00488

Gnomad OTH exome AF: 0.00473

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00389 AC: 587 AN: 151024 Hom.: 4 Cov.: 0 AF XY: 0.00398 AC XY: 318 AN XY: 79968

African (AFR) AF: 0.000600 AC: 3 AN: 5002

American (AMR) AF: 0.00328 AC: 22 AN: 6710

Ashkenazi Jewish (ASJ) AF: 0.00648 AC: 26 AN: 4010

East Asian (EAS) AF: 0.00 AC: 0 AN: 6978

South Asian (SAS) AF: 0.00403 AC: 96 AN: 23834

European-Finnish (FIN) AF: 0.000288 AC: 2 AN: 6944

Middle Eastern (MID) AF: 0.0144 AC: 9 AN: 626

European-Non Finnish (NFE) AF: 0.00456 AC: 405 AN: 88742

Other (OTH) AF: 0.00293 AC: 24 AN: 8178

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00291 AC: 262 AN: 90086 Hom.: 0 Cov.: 11 AF XY: 0.00279 AC XY: 108 AN XY: 38740

African (AFR) AF: 0.000833 AC: 18 AN: 21612

American (AMR) AF: 0.00298 AC: 24 AN: 8060

Ashkenazi Jewish (ASJ) AF: 0.00392 AC: 10 AN: 2548

East Asian (EAS) AF: 0.00 AC: 0 AN: 3350

South Asian (SAS) AF: 0.000920 AC: 2 AN: 2174

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4808

Middle Eastern (MID) AF: 0.00413 AC: 1 AN: 242

European-Non Finnish (NFE) AF: 0.00444 AC: 202 AN: 45506

Other (OTH) AF: 0.00170 AC: 2 AN: 1174

Alfa AF: 0.00282 Hom.: 1

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.0
DANN	Benign	0.71
PhyloP100		-0.047
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs1173080093; hg19: chr16-89334621;