2-97113750-G-A

Variant summary

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

The NM_001354587.1(ANKRD36):​c.11G>A​(p.Gly4Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,608,904 control chromosomes in the GnomAD database, including 33 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 (★).

Frequency

Genomes: 𝑓 0.0022 ( 5 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 28 hom. )

Consequence

ANKRD36
NM_001354587.1 missense

Scores

1
18

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.09
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=0.0074519515).
BP6
Variant 2-97113750-G-A is Benign according to our data. Variant chr2-97113750-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2651156.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-97113750-G-A is described in Lovd as [Likely_benign].
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.11G>A p.Gly4Asp 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.11G>A p.Gly4Asp missense_variant Exon 1 of 76 5 NM_001354587.1 ENSP00000391950.4 A6QL64-1
ANKRD36ENST00000452478.2 linkn.199G>A non_coding_transcript_exon_variant Exon 1 of 3 1
ANKRD36ENST00000461153.7 linkc.11G>A p.Gly4Asp missense_variant Exon 1 of 75 5 ENSP00000419530.3 A6QL64-1
ANKRD36ENST00000652721.1 linkc.11G>A p.Gly4Asp missense_variant Exon 1 of 76 ENSP00000498611.1 A6QL64-1

Frequencies

GnomAD3 genomes
AF:
0.00220
AC:
334
AN:
151752
Hom.:
5
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000579
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00315
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000598
Gnomad SAS
AF:
0.000841
Gnomad FIN
AF:
0.000854
Gnomad MID
AF:
0.0191
Gnomad NFE
AF:
0.00340
Gnomad OTH
AF:
0.00431
GnomAD3 exomes
AF:
0.000687
AC:
170
AN:
247564
Hom.:
4
AF XY:
0.000669
AC XY:
90
AN XY:
134554
show subpopulations
Gnomad AFR exome
AF:
0.000130
Gnomad AMR exome
AF:
0.00105
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000197
Gnomad FIN exome
AF:
0.000186
Gnomad NFE exome
AF:
0.00105
Gnomad OTH exome
AF:
0.000667
GnomAD4 exome
AF:
0.00116
AC:
1689
AN:
1457048
Hom.:
28
Cov.:
32
AF XY:
0.00122
AC XY:
882
AN XY:
724768
show subpopulations
Gnomad4 AFR exome
AF:
0.000120
Gnomad4 AMR exome
AF:
0.00177
Gnomad4 ASJ exome
AF:
0.000115
Gnomad4 EAS exome
AF:
0.0000256
Gnomad4 SAS exome
AF:
0.000604
Gnomad4 FIN exome
AF:
0.000772
Gnomad4 NFE exome
AF:
0.00121
Gnomad4 OTH exome
AF:
0.00208
GnomAD4 genome
AF:
0.00220
AC:
334
AN:
151856
Hom.:
5
Cov.:
32
AF XY:
0.00208
AC XY:
154
AN XY:
74146
show subpopulations
Gnomad4 AFR
AF:
0.000577
Gnomad4 AMR
AF:
0.00315
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000599
Gnomad4 SAS
AF:
0.000841
Gnomad4 FIN
AF:
0.000854
Gnomad4 NFE
AF:
0.00340
Gnomad4 OTH
AF:
0.00430
Alfa
AF:
0.00141
Hom.:
1
Bravo
AF:
0.00260
ExAC
AF:
0.000323
AC:
39

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
0.16
BayesDel_addAF
Benign
-0.69
T
BayesDel_noAF
Benign
-0.76
CADD
Benign
0.10
DANN
Benign
0.76
DEOGEN2
Benign
0.0059
.;.;.;T
Eigen
Benign
-2.1
Eigen_PC
Benign
-2.2
FATHMM_MKL
Benign
0.014
N
LIST_S2
Benign
0.20
T;T;T;T
M_CAP
Benign
0.0012
T
MetaRNN
Benign
0.0075
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.34
.;.;.;N
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-0.83
.;N;.;N
REVEL
Benign
0.017
Sift
Benign
0.96
.;T;.;T
Sift4G
Benign
0.87
.;T;T;T
Polyphen
0.0
.;.;.;B
Vest4
0.12, 0.18, 0.14
MVP
0.030
ClinPred
0.00092
T
GERP RS
-0.91
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.083

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: rs2315151; hg19: chr2-97779487; COSMIC: COSV70737144; API