NM_001394998.1:c.1575+4358A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394998.1(TANC2):c.1575+4358A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,054 control chromosomes in the GnomAD database, including 29,980 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.60 ( 29980 hom., cov: 32)
Consequence
TANC2
NM_001394998.1 intron
NM_001394998.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.471
Publications
7 publications found
Genes affected
TANC2 (HGNC:30212): (tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2) Predicted to be involved in dense core granule cytoskeletal transport; regulation of dendritic spine development; and regulation of dendritic spine morphogenesis. Predicted to act upstream of or within in utero embryonic development. Located in dendritic spine. [provided by Alliance of Genome Resources, Apr 2022]
TANC2 Gene-Disease associations (from GenCC):
- intellectual developmental disorder with autistic features and language delay, with or without seizuresInheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, LIMITED Submitted by: Illumina, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics, ClinGen
- syndromic intellectual disabilityInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TANC2 | NM_001394998.1 | c.1575+4358A>G | intron_variant | Intron 11 of 27 | ENST00000689528.1 | NP_001381927.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TANC2 | ENST00000689528.1 | c.1575+4358A>G | intron_variant | Intron 11 of 27 | NM_001394998.1 | ENSP00000510600.1 |
Frequencies
GnomAD3 genomes AF: 0.600 AC: 91154AN: 151936Hom.: 29918 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
91154
AN:
151936
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.600 AC: 91273AN: 152054Hom.: 29980 Cov.: 32 AF XY: 0.595 AC XY: 44196AN XY: 74302 show subpopulations
GnomAD4 genome
AF:
AC:
91273
AN:
152054
Hom.:
Cov.:
32
AF XY:
AC XY:
44196
AN XY:
74302
show subpopulations
African (AFR)
AF:
AC:
36160
AN:
41502
American (AMR)
AF:
AC:
7297
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
1661
AN:
3466
East Asian (EAS)
AF:
AC:
854
AN:
5168
South Asian (SAS)
AF:
AC:
2372
AN:
4814
European-Finnish (FIN)
AF:
AC:
6004
AN:
10564
Middle Eastern (MID)
AF:
AC:
145
AN:
294
European-Non Finnish (NFE)
AF:
AC:
35096
AN:
67962
Other (OTH)
AF:
AC:
1141
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1625
3251
4876
6502
8127
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
728
1456
2184
2912
3640
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1439
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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