rs16957849
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015226.3(CLEC16A):c.598+220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 628,106 control chromosomes in the GnomAD database, including 14,954 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 0.21 ( 3566 hom., cov: 32)
Exomes 𝑓: 0.21 ( 11388 hom. )
Consequence
CLEC16A
NM_015226.3 intron
NM_015226.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.150
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC16A | NM_015226.3 | c.598+220T>C | intron_variant | ENST00000409790.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC16A | ENST00000409790.6 | c.598+220T>C | intron_variant | 5 | NM_015226.3 | A1 | |||
CLEC16A | ENST00000409552.4 | c.598+220T>C | intron_variant | 1 | |||||
CLEC16A | ENST00000703130.1 | c.598+220T>C | intron_variant | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.210 AC: 31865AN: 152042Hom.: 3559 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
31865
AN:
152042
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:
GnomAD4 exome AF: 0.214 AC: 101907AN: 475946Hom.: 11388 AF XY: 0.216 AC XY: 48312AN XY: 224040
GnomAD4 exome
AF:
AC:
101907
AN:
475946
Hom.:
AF XY:
AC XY:
48312
AN XY:
224040
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.210 AC: 31894AN: 152160Hom.: 3566 Cov.: 32 AF XY: 0.207 AC XY: 15413AN XY: 74400
GnomAD4 genome
?
AF:
AC:
31894
AN:
152160
Hom.:
Cov.:
32
AF XY:
AC XY:
15413
AN XY:
74400
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
599
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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