2-97194844-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5

The NM_001354587.1(ANKRD36):​c.2479-1G>A variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000594 in 1,591,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (no stars).

Frequency

Genomes: 𝑓 0.00074 ( 0 hom., cov: 45)
Exomes 𝑓: 0.00058 ( 0 hom. )

Consequence

ANKRD36
NM_001354587.1 splice_acceptor, intron

Scores

7
Splicing: ADA: 1.000
2

Clinical Significance

Likely pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 2.30
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 Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 2-97194844-G-A is Pathogenic according to our data. Variant chr2-97194844-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 917512.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ANKRD36NM_001354587.1 linkc.2479-1G>A splice_acceptor_variant, intron_variant Intron 39 of 75 ENST00000420699.9 NP_001341516.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ANKRD36ENST00000420699.9 linkc.2479-1G>A splice_acceptor_variant, intron_variant Intron 39 of 75 5 NM_001354587.1 ENSP00000391950.4 A6QL64-1
ANKRD36ENST00000461153.7 linkc.2479-1G>A splice_acceptor_variant, intron_variant Intron 39 of 74 5 ENSP00000419530.3 A6QL64-1
ANKRD36ENST00000652721.1 linkc.2479-1G>A splice_acceptor_variant, intron_variant Intron 39 of 75 ENSP00000498611.1 A6QL64-1

Frequencies

GnomAD3 genomes
AF:
0.000744
AC:
113
AN:
151920
Hom.:
0
Cov.:
45
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000985
Gnomad ASJ
AF:
0.0194
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000209
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000324
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00118
AC:
258
AN:
218424
Hom.:
0
AF XY:
0.00112
AC XY:
133
AN XY:
118696
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000950
Gnomad ASJ exome
AF:
0.0193
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000220
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000358
Gnomad OTH exome
AF:
0.000717
GnomAD4 exome
AF:
0.000579
AC:
834
AN:
1439462
Hom.:
0
Cov.:
38
AF XY:
0.000589
AC XY:
421
AN XY:
715168
show subpopulations
Gnomad4 AFR exome
AF:
0.0000608
Gnomad4 AMR exome
AF:
0.000844
Gnomad4 ASJ exome
AF:
0.0181
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000335
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000178
Gnomad4 OTH exome
AF:
0.00164
GnomAD4 genome
AF:
0.000737
AC:
112
AN:
152038
Hom.:
0
Cov.:
45
AF XY:
0.000632
AC XY:
47
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.0000482
Gnomad4 AMR
AF:
0.000984
Gnomad4 ASJ
AF:
0.0194
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000209
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000324
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00241
Hom.:
0
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.00126
AC:
4
ExAC
AF:
0.000795
AC:
95

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Hearing loss, autosomal recessive Pathogenic:1
Jul 06, 2019
Laboratory of Prof. Karen Avraham, Tel Aviv University
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: research

Recessive, compound heterozygous with NM_001354587.1: 2589T>G; congenital, moderate-severe progressive SNHL -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.46
T
BayesDel_noAF
Benign
-0.90
CADD
Benign
20
DANN
Benign
0.38
Eigen
Benign
0.059
Eigen_PC
Benign
-0.40
FATHMM_MKL
Benign
0.023
N
GERP RS
0.66
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.73
SpliceAI score (max)
0.94
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.49
Position offset: 2
DS_AL_spliceai
0.94
Position offset: 1

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: rs200852589; hg19: chr2-97860581; API