2-97113752-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001354587.1(ANKRD36):ā€‹c.13A>Gā€‹(p.Lys5Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00131 in 1,588,970 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: š‘“ 0.0025 ( 5 hom., cov: 31)
Exomes š‘“: 0.0012 ( 29 hom. )

Consequence

ANKRD36
NM_001354587.1 missense

Scores

1
18

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.52
Variant links:
Genes affected
ANKRD36 (HGNC:24079): (ankyrin repeat domain 36)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.008763403).
BP6
Variant 2-97113752-A-G is Benign according to our data. Variant chr2-97113752-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2651157.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ANKRD36NM_001354587.1 linkc.13A>G p.Lys5Glu missense_variant Exon 1 of 76 ENST00000420699.9 NP_001341516.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ANKRD36ENST00000420699.9 linkc.13A>G p.Lys5Glu missense_variant Exon 1 of 76 5 NM_001354587.1 ENSP00000391950.4 A6QL64-1
ANKRD36ENST00000452478.2 linkn.201A>G non_coding_transcript_exon_variant Exon 1 of 3 1
ANKRD36ENST00000461153.7 linkc.13A>G p.Lys5Glu missense_variant Exon 1 of 75 5 ENSP00000419530.3 A6QL64-1
ANKRD36ENST00000652721.1 linkc.13A>G p.Lys5Glu missense_variant Exon 1 of 76 ENSP00000498611.1 A6QL64-1

Frequencies

GnomAD3 genomes
AF:
0.00251
AC:
333
AN:
132414
Hom.:
5
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000595
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00344
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000601
Gnomad SAS
AF:
0.00108
Gnomad FIN
AF:
0.00150
Gnomad MID
AF:
0.0194
Gnomad NFE
AF:
0.00407
Gnomad OTH
AF:
0.00478
GnomAD3 exomes
AF:
0.00101
AC:
216
AN:
213990
Hom.:
4
AF XY:
0.00102
AC XY:
119
AN XY:
116420
show subpopulations
Gnomad AFR exome
AF:
0.000133
Gnomad AMR exome
AF:
0.00141
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000337
Gnomad FIN exome
AF:
0.000323
Gnomad NFE exome
AF:
0.00160
Gnomad OTH exome
AF:
0.00133
GnomAD4 exome
AF:
0.00120
AC:
1755
AN:
1456456
Hom.:
29
Cov.:
32
AF XY:
0.00126
AC XY:
912
AN XY:
724492
show subpopulations
Gnomad4 AFR exome
AF:
0.000120
Gnomad4 AMR exome
AF:
0.00184
Gnomad4 ASJ exome
AF:
0.000115
Gnomad4 EAS exome
AF:
0.0000256
Gnomad4 SAS exome
AF:
0.000709
Gnomad4 FIN exome
AF:
0.000772
Gnomad4 NFE exome
AF:
0.00125
Gnomad4 OTH exome
AF:
0.00221
GnomAD4 genome
AF:
0.00251
AC:
332
AN:
132514
Hom.:
5
Cov.:
31
AF XY:
0.00237
AC XY:
152
AN XY:
64054
show subpopulations
Gnomad4 AFR
AF:
0.000593
Gnomad4 AMR
AF:
0.00343
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000603
Gnomad4 SAS
AF:
0.000865
Gnomad4 FIN
AF:
0.00150
Gnomad4 NFE
AF:
0.00407
Gnomad4 OTH
AF:
0.00477
Alfa
AF:
0.00173
Hom.:
0
Bravo
AF:
0.00262
ExAC
AF:
0.000344
AC:
40

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Feb 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

ANKRD36: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Benign
-0.39
T
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.0060
DANN
Benign
0.12
DEOGEN2
Benign
0.0033
.;.;.;T
Eigen
Benign
-1.8
Eigen_PC
Benign
-1.9
FATHMM_MKL
Benign
0.010
N
LIST_S2
Benign
0.23
T;T;T;T
M_CAP
Benign
0.0017
T
MetaRNN
Benign
0.0088
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.69
.;.;.;N
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
0.67
.;N;.;N
REVEL
Benign
0.010
Sift
Benign
1.0
.;T;.;T
Sift4G
Benign
1.0
.;T;T;T
Polyphen
0.0
.;.;.;B
Vest4
0.038, 0.083, 0.059
MVP
0.076
ClinPred
0.0042
T
GERP RS
-0.91
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.063

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: rs774044606; hg19: chr2-97779489; COSMIC: COSV70741006; API