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GeneBe

12-110018396-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_033121.2(ANKRD13A):​c.452G>A​(p.Ser151Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000212 in 1,614,012 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 0 hom. )

Consequence

ANKRD13A
NM_033121.2 missense

Scores

3
6
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.94
Variant links:
Genes affected
ANKRD13A (HGNC:21268): (ankyrin repeat domain 13A) Enables ubiquitin-dependent protein binding activity. Involved in negative regulation of protein localization to endosome and negative regulation of receptor internalization. Located in late endosome; perinuclear region of cytoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.12355083).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ANKRD13ANM_033121.2 linkuse as main transcriptc.452G>A p.Ser151Asn missense_variant 5/15 ENST00000261739.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANKRD13AENST00000261739.9 linkuse as main transcriptc.452G>A p.Ser151Asn missense_variant 5/151 NM_033121.2 P1
ANKRD13AENST00000550404.1 linkuse as main transcriptn.711G>A non_coding_transcript_exon_variant 5/71
ANKRD13AENST00000553025.5 linkuse as main transcriptc.188G>A p.Ser63Asn missense_variant, NMD_transcript_variant 5/121
ANKRD13AENST00000547639.5 linkuse as main transcriptc.14G>A p.Ser5Asn missense_variant 1/85

Frequencies

GnomAD3 genomes
AF:
0.000237
AC:
36
AN:
152164
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00245
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000132
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000441
AC:
111
AN:
251456
Hom.:
0
AF XY:
0.000412
AC XY:
56
AN XY:
135904
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00189
Gnomad NFE exome
AF:
0.000580
Gnomad OTH exome
AF:
0.000326
GnomAD4 exome
AF:
0.000209
AC:
306
AN:
1461848
Hom.:
0
Cov.:
31
AF XY:
0.000205
AC XY:
149
AN XY:
727224
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00159
Gnomad4 NFE exome
AF:
0.000186
Gnomad4 OTH exome
AF:
0.000232
GnomAD4 genome
AF:
0.000237
AC:
36
AN:
152164
Hom.:
0
Cov.:
32
AF XY:
0.000269
AC XY:
20
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00245
Gnomad4 NFE
AF:
0.000132
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000168
Hom.:
0
Bravo
AF:
0.0000756
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.000349
AC:
3
ExAC
AF:
0.000568
AC:
69
EpiCase
AF:
0.000109
EpiControl
AF:
0.000237

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 13, 2021The c.452G>A (p.S151N) alteration is located in exon 5 (coding exon 5) of the ANKRD13A gene. This alteration results from a G to A substitution at nucleotide position 452, causing the serine (S) at amino acid position 151 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.36
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.29
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Benign
0.028
T
Eigen
Uncertain
0.64
Eigen_PC
Pathogenic
0.70
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.91
D
M_CAP
Benign
0.025
D
MetaRNN
Benign
0.12
T
MetaSVM
Uncertain
-0.25
T
MutationAssessor
Uncertain
2.4
M
MutationTaster
Benign
1.0
D
PrimateAI
Pathogenic
0.81
D
PROVEAN
Benign
-1.8
N
REVEL
Benign
0.27
Sift
Benign
0.080
T
Sift4G
Benign
0.11
T
Polyphen
1.0
D
Vest4
0.68
MVP
0.69
MPC
0.88
ClinPred
0.11
T
GERP RS
5.6
Varity_R
0.36
gMVP
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs370163748; hg19: chr12-110456201; API