rs11074952
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015226.3(CLEC16A):c.2473+803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,034 control chromosomes in the GnomAD database, including 7,042 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 0.30 ( 7042 hom., cov: 32)
Consequence
CLEC16A
NM_015226.3 intron
NM_015226.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0950
Publications
5 publications found
Genes affected
CLEC16A (HGNC:29013): (C-type lectin domain containing 16A) This gene encodes a member of the C-type lectin domain containing family. Single nucleotide polymorphisms in introns of this gene have been associated with diabetes mellitus, multiple sclerosis and rheumatoid arthritis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
CLEC16A Gene-Disease associations (from GenCC):
- schizophreniaInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
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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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.302 AC: 45830AN: 151916Hom.: 7042 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
45830
AN:
151916
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: 0.302 AC: 45852AN: 152034Hom.: 7042 Cov.: 32 AF XY: 0.298 AC XY: 22164AN XY: 74320 show subpopulations
GnomAD4 genome
AF:
AC:
45852
AN:
152034
Hom.:
Cov.:
32
AF XY:
AC XY:
22164
AN XY:
74320
show subpopulations
African (AFR)
AF:
AC:
14937
AN:
41446
American (AMR)
AF:
AC:
3883
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
702
AN:
3470
East Asian (EAS)
AF:
AC:
1141
AN:
5160
South Asian (SAS)
AF:
AC:
1471
AN:
4820
European-Finnish (FIN)
AF:
AC:
2580
AN:
10574
Middle Eastern (MID)
AF:
AC:
97
AN:
294
European-Non Finnish (NFE)
AF:
AC:
20104
AN:
67966
Other (OTH)
AF:
AC:
602
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1619
3238
4856
6475
8094
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
895
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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