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rs12708716

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015226.3(CLEC16A):c.2116+24994A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,140 control chromosomes in the GnomAD database, including 10,625 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 0.37 ( 10625 hom., cov: 33)

Consequence

CLEC16A
NM_015226.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CLEC16ANM_015226.3 linkuse as main transcriptc.2116+24994A>G intron_variant ENST00000409790.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLEC16AENST00000409790.6 linkuse as main transcriptc.2116+24994A>G intron_variant 5 NM_015226.3 A1Q2KHT3-1

Frequencies

GnomAD3 genomes
AF:
0.370
AC:
56261
AN:
152022
Hom.:
10591
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.422
Gnomad AMI
AF:
0.294
Gnomad AMR
AF:
0.311
Gnomad ASJ
AF:
0.456
Gnomad EAS
AF:
0.217
Gnomad SAS
AF:
0.393
Gnomad FIN
AF:
0.357
Gnomad MID
AF:
0.405
Gnomad NFE
AF:
0.360
Gnomad OTH
AF:
0.380
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.370
AC:
56348
AN:
152140
Hom.:
10625
Cov.:
33
AF XY:
0.368
AC XY:
27333
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.422
Gnomad4 AMR
AF:
0.311
Gnomad4 ASJ
AF:
0.456
Gnomad4 EAS
AF:
0.217
Gnomad4 SAS
AF:
0.394
Gnomad4 FIN
AF:
0.357
Gnomad4 NFE
AF:
0.360
Gnomad4 OTH
AF:
0.384
Alfa
AF:
0.358
Hom.:
11855
Bravo
AF:
0.367
Asia WGS
AF:
0.345
AC:
1198
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
3.0
Dann
Benign
0.49

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: rs12708716; hg19: chr16-11179873; API