GeneBe

rs369403534

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_024669.3(ANKRD55):​c.1195G>T​(p.Asp399Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D399N) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ANKRD55
NM_024669.3 missense

Scores

3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.66

Publications

0 publications found
Variant links:
Genes affected
ANKRD55 (HGNC:25681): (ankyrin repeat domain 55)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.16013017).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024669.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ANKRD55
NM_024669.3
MANE Select
c.1195G>Tp.Asp399Tyr
missense
Exon 10 of 12NP_078945.2Q3KP44-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ANKRD55
ENST00000341048.9
TSL:2 MANE Select
c.1195G>Tp.Asp399Tyr
missense
Exon 10 of 12ENSP00000342295.4Q3KP44-1
ANKRD55
ENST00000434982.2
TSL:1
c.331G>Tp.Asp111Tyr
missense
Exon 2 of 4ENSP00000429421.1Q3KP44-2
ANKRD55
ENST00000504958.6
TSL:5
c.1066G>Tp.Asp356Tyr
missense
Exon 8 of 10ENSP00000424230.1D6RBD3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00000400
AC:
1
AN:
250282
AF XY:
0.00000739
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000883
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1460818
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
726744
African (AFR)
AF:
0.00
AC:
0
AN:
33334
American (AMR)
AF:
0.00
AC:
0
AN:
44510
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26068
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39698
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86094
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53390
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5762
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1111648
Other (OTH)
AF:
0.00
AC:
0
AN:
60314
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.096
BayesDel_addAF
Benign
-0.080
T
BayesDel_noAF
Benign
-0.35
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.035
T
Eigen
Benign
-0.026
Eigen_PC
Benign
0.014
FATHMM_MKL
Benign
0.44
N
LIST_S2
Benign
0.77
T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.16
T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
1.8
L
PhyloP100
1.7
PrimateAI
Benign
0.40
T
PROVEAN
Benign
-0.69
N
REVEL
Benign
0.093
Sift
Uncertain
0.0010
D
Sift4G
Uncertain
0.0060
D
Vest4
0.28
MVP
0.51
MPC
0.53
ClinPred
0.81
D
GERP RS
3.6
Varity_R
0.15
gMVP
0.62
Mutation Taster
=84/16
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs369403534; hg19: chr5-55407380; API