rs753852

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013275.6(ANKRD11):​c.-60+38273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,946 control chromosomes in the GnomAD database, including 22,633 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 0.54 ( 22633 hom., cov: 32)

Consequence

ANKRD11
NM_013275.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.668
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC128462377NM_001416403.1 linkuse as main transcriptc.9+38273C>T intron_variant ENST00000711617.1
ANKRD11NM_013275.6 linkuse as main transcriptc.-60+38273C>T intron_variant ENST00000301030.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANKRD11ENST00000301030.10 linkuse as main transcriptc.-60+38273C>T intron_variant 5 NM_013275.6 P1
ENST00000711617.1 linkuse as main transcriptc.9+38273C>T intron_variant NM_001416403.1 A2

Frequencies

GnomAD3 genomes
AF:
0.543
AC:
82403
AN:
151828
Hom.:
22611
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.484
Gnomad AMI
AF:
0.619
Gnomad AMR
AF:
0.565
Gnomad ASJ
AF:
0.695
Gnomad EAS
AF:
0.590
Gnomad SAS
AF:
0.546
Gnomad FIN
AF:
0.463
Gnomad MID
AF:
0.741
Gnomad NFE
AF:
0.570
Gnomad OTH
AF:
0.622
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.543
AC:
82467
AN:
151946
Hom.:
22633
Cov.:
32
AF XY:
0.540
AC XY:
40070
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.484
Gnomad4 AMR
AF:
0.565
Gnomad4 ASJ
AF:
0.695
Gnomad4 EAS
AF:
0.590
Gnomad4 SAS
AF:
0.547
Gnomad4 FIN
AF:
0.463
Gnomad4 NFE
AF:
0.570
Gnomad4 OTH
AF:
0.624
Alfa
AF:
0.552
Hom.:
3299
Bravo
AF:
0.546
Asia WGS
AF:
0.592
AC:
2059
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.5
DANN
Benign
0.41

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.

Other links and lift over

dbSNP: rs753852; hg19: chr16-89446419; API