16-11113865-T-C

Variant summary

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

The NM_015226.3(CLEC16A):​c.2117-6750T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,972 control chromosomes in the GnomAD database, including 19,513 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 0.49 ( 19513 hom., cov: 32)

Consequence

CLEC16A
NM_015226.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.568
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]

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=-0.62).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CLEC16ANM_015226.3 linkuse as main transcriptc.2117-6750T>C intron_variant ENST00000409790.6 NP_056041.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CLEC16AENST00000409790.6 linkuse as main transcriptc.2117-6750T>C intron_variant 5 NM_015226.3 ENSP00000387122 A1Q2KHT3-1

Frequencies

GnomAD3 genomes
AF:
0.494
AC:
75032
AN:
151854
Hom.:
19471
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.666
Gnomad AMI
AF:
0.419
Gnomad AMR
AF:
0.405
Gnomad ASJ
AF:
0.534
Gnomad EAS
AF:
0.354
Gnomad SAS
AF:
0.436
Gnomad FIN
AF:
0.404
Gnomad MID
AF:
0.491
Gnomad NFE
AF:
0.437
Gnomad OTH
AF:
0.502
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.494
AC:
75130
AN:
151972
Hom.:
19513
Cov.:
32
AF XY:
0.489
AC XY:
36332
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.666
Gnomad4 AMR
AF:
0.405
Gnomad4 ASJ
AF:
0.534
Gnomad4 EAS
AF:
0.354
Gnomad4 SAS
AF:
0.437
Gnomad4 FIN
AF:
0.404
Gnomad4 NFE
AF:
0.437
Gnomad4 OTH
AF:
0.504
Alfa
AF:
0.386
Hom.:
2793
Bravo
AF:
0.501
Asia WGS
AF:
0.445
AC:
1546
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
CADD
Benign
16
DANN
Benign
0.67

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: rs7203150; hg19: chr16-11207722; API