2-97113741-T-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PVS1_SupportingBP6_ModerateBS2

The NM_001354587.1(ANKRD36):​c.2T>A​(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 1,608,552 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 25 hom. )

Consequence

ANKRD36
NM_001354587.1 start_lost

Scores

3
13

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.85
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 Likely_benign. Variant got -5 ACMG points.

PVS1
Start lost variant, no pathogenic variants between lost start and next in-frame start position. Next in-frame start position is after 36 CDS bases. Genomic position: 97113775. Lost 0.006 part of the original CDS.
BP6
Variant 2-97113741-T-A is Benign according to our data. Variant chr2-97113741-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2651155.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ANKRD36NM_001354587.1 linkc.2T>A p.Met1? start_lost 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.2T>A p.Met1? start_lost Exon 1 of 76 5 NM_001354587.1 ENSP00000391950.4 A6QL64-1
ANKRD36ENST00000452478.2 linkn.190T>A non_coding_transcript_exon_variant Exon 1 of 3 1
ANKRD36ENST00000461153.7 linkc.2T>A p.Met1? start_lost Exon 1 of 75 5 ENSP00000419530.3 A6QL64-1
ANKRD36ENST00000652721.1 linkc.2T>A p.Met1? start_lost Exon 1 of 76 ENSP00000498611.1 A6QL64-1

Frequencies

GnomAD3 genomes
AF:
0.00223
AC:
334
AN:
150020
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000604
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00297
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000200
Gnomad SAS
AF:
0.000841
Gnomad FIN
AF:
0.00123
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.00345
Gnomad OTH
AF:
0.00434
GnomAD3 exomes
AF:
0.000666
AC:
163
AN:
244622
Hom.:
3
AF XY:
0.000631
AC XY:
84
AN XY:
133104
show subpopulations
Gnomad AFR exome
AF:
0.0000650
Gnomad AMR exome
AF:
0.000937
Gnomad ASJ exome
AF:
0.000100
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000164
Gnomad FIN exome
AF:
0.000995
Gnomad NFE exome
AF:
0.000901
Gnomad OTH exome
AF:
0.000672
GnomAD4 exome
AF:
0.00114
AC:
1662
AN:
1458430
Hom.:
25
Cov.:
31
AF XY:
0.00120
AC XY:
870
AN XY:
725426
show subpopulations
Gnomad4 AFR exome
AF:
0.0000896
Gnomad4 AMR exome
AF:
0.00160
Gnomad4 ASJ exome
AF:
0.000153
Gnomad4 EAS exome
AF:
0.0000256
Gnomad4 SAS exome
AF:
0.000570
Gnomad4 FIN exome
AF:
0.00109
Gnomad4 NFE exome
AF:
0.00118
Gnomad4 OTH exome
AF:
0.00206
GnomAD4 genome
AF:
0.00222
AC:
334
AN:
150122
Hom.:
3
Cov.:
32
AF XY:
0.00212
AC XY:
155
AN XY:
73112
show subpopulations
Gnomad4 AFR
AF:
0.000602
Gnomad4 AMR
AF:
0.00297
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000200
Gnomad4 SAS
AF:
0.000842
Gnomad4 FIN
AF:
0.00123
Gnomad4 NFE
AF:
0.00345
Gnomad4 OTH
AF:
0.00434
Alfa
AF:
0.00204
Hom.:
1
ExAC
AF:
0.000774
AC:
93

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
BayesDel_addAF
Benign
-0.54
T
BayesDel_noAF
Benign
-0.61
CADD
Benign
7.0
DANN
Benign
0.76
DEOGEN2
Benign
0.00086
.;.;.;T
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.036
N
LIST_S2
Uncertain
0.90
D;D;D;D
M_CAP
Benign
0.0011
T
MetaRNN
Benign
0.020
T;T;T;T
MetaSVM
Benign
-0.99
T
PROVEAN
Benign
0.12
.;N;.;N
REVEL
Benign
0.052
Sift
Uncertain
0.0010
.;D;.;D
Sift4G
Uncertain
0.0030
.;D;D;D
Polyphen
0.051
.;.;.;B
Vest4
0.23, 0.25, 0.22
MVP
0.23
ClinPred
0.0099
T
GERP RS
-0.91
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.1
Varity_R
0.44

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: rs200032015; hg19: chr2-97779478; COSMIC: COSV70739232; API