2-95853744-C-T

Variant summary

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

The NM_001393982.1(ANKRD36C):​c.6136G>A​(p.Asp2046Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00758 in 1,594,738 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0050 ( 2 hom., cov: 30)
Exomes 𝑓: 0.0079 ( 75 hom. )

Consequence

ANKRD36C
NM_001393982.1 missense

Scores

1
1
14

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.57
Variant links:
Genes affected
ANKRD36C (HGNC:32946): (ankyrin repeat domain 36C)

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=0.007240534).
BP6
Variant 2-95853744-C-T is Benign according to our data. Variant chr2-95853744-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651123.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ANKRD36CNM_001393982.1 linkc.6136G>A p.Asp2046Asn missense_variant Exon 84 of 88 ENST00000295246.7 NP_001380911.1
ANKRD36CNM_001310154.3 linkc.6211G>A p.Asp2071Asn missense_variant Exon 85 of 89 NP_001297083.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ANKRD36CENST00000295246.7 linkc.6136G>A p.Asp2046Asn missense_variant Exon 84 of 88 5 NM_001393982.1 ENSP00000295246.7 A0A8J8YUB5
ANKRD36CENST00000612359.4 linkc.190G>A p.Asp64Asn missense_variant Exon 2 of 6 1 ENSP00000485004.1 A0A0C4DH05
ANKRD36CENST00000488721.5 linkn.1286G>A non_coding_transcript_exon_variant Exon 4 of 4 1
ANKRD36CENST00000456556.5 linkc.5113G>A p.Asp1705Asn missense_variant Exon 64 of 67 5 ENSP00000403302.1 Q5JPF3-1

Frequencies

GnomAD3 genomes
AF:
0.00500
AC:
760
AN:
152078
Hom.:
2
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00130
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.00210
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00539
Gnomad FIN
AF:
0.00764
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.00818
Gnomad OTH
AF:
0.00383
GnomAD3 exomes
AF:
0.00544
AC:
1066
AN:
196092
Hom.:
4
AF XY:
0.00582
AC XY:
605
AN XY:
103952
show subpopulations
Gnomad AFR exome
AF:
0.00115
Gnomad AMR exome
AF:
0.00216
Gnomad ASJ exome
AF:
0.000218
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00525
Gnomad FIN exome
AF:
0.00694
Gnomad NFE exome
AF:
0.00844
Gnomad OTH exome
AF:
0.00667
GnomAD4 exome
AF:
0.00785
AC:
11324
AN:
1442542
Hom.:
75
Cov.:
30
AF XY:
0.00784
AC XY:
5611
AN XY:
715792
show subpopulations
Gnomad4 AFR exome
AF:
0.00117
Gnomad4 AMR exome
AF:
0.00198
Gnomad4 ASJ exome
AF:
0.000232
Gnomad4 EAS exome
AF:
0.0000255
Gnomad4 SAS exome
AF:
0.00599
Gnomad4 FIN exome
AF:
0.00702
Gnomad4 NFE exome
AF:
0.00894
Gnomad4 OTH exome
AF:
0.00758
GnomAD4 genome
AF:
0.00499
AC:
760
AN:
152196
Hom.:
2
Cov.:
30
AF XY:
0.00504
AC XY:
375
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.00130
Gnomad4 AMR
AF:
0.00209
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00540
Gnomad4 FIN
AF:
0.00764
Gnomad4 NFE
AF:
0.00818
Gnomad4 OTH
AF:
0.00379
Alfa
AF:
0.00709
Hom.:
1
Bravo
AF:
0.00432
ExAC
AF:
0.00455
AC:
548

ClinVar

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

Submissions by phenotype

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

ANKRD36C: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.64
T
BayesDel_noAF
Benign
-0.68
CADD
Benign
18
DANN
Benign
0.97
DEOGEN2
Benign
0.0091
.;T
Eigen
Benign
-0.41
Eigen_PC
Benign
-0.52
FATHMM_MKL
Benign
0.087
N
LIST_S2
Benign
0.51
T;T
MetaRNN
Benign
0.0072
T;T
MetaSVM
Benign
-1.0
T
PROVEAN
Uncertain
-3.3
.;D
REVEL
Benign
0.042
Sift
Benign
0.042
.;D
Sift4G
Pathogenic
0.0
D;T
Vest4
0.11
MVP
0.15
ClinPred
0.028
T
GERP RS
-0.10
Varity_R
0.13
gMVP
0.0066

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: rs200478637; hg19: chr2-96519492; API