Variant 16-11020335-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_015226.3(CLEC16A):c.1436+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0194 in 1,599,846 control chromosomes in the GnomAD database, including 393 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 0.016 ( 33 hom., cov: 33)

Exomes 𝑓: 0.020 ( 360 hom. )

Consequence

CLEC16A
NM_015226.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.157

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]

CLEC16A links:

CLEC16A (HGNC:):

CLEC16A links:

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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=-0.87).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0157 (2395/152288) while in subpopulation NFE AF= 0.0238 (1619/68012). AF 95% confidence interval is 0.0228. There are 33 homozygotes in gnomad4. There are 1210 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 33 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3 linkuse as main transcript	c.1436+10C>T		intron_variant		ENST00000409790.6	NP_056041.1	Q2KHT3-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CLEC16A	ENST00000409790.6 linkuse as main transcript	c.1436+10C>T	intron_variant	5	NM_015226.3	ENSP00000387122.1	Q2KHT3-1
CLEC16A	ENST00000409552.4 linkuse as main transcript	c.1382+10C>T	intron_variant	1		ENSP00000386495.3	Q2KHT3-2
CLEC16A	ENST00000703130.1 linkuse as main transcript	c.1430+10C>T	intron_variant			ENSP00000515187.1	A0A8V8TR67
CLEC16A	ENST00000494853.1 linkuse as main transcript	n.911+10C>T	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.0157

AC:

2395

AN:

152170

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00420

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.00850

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.0389

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0238

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.0164

AC:

3609

AN:

219940

Hom.:

AF XY:

0.0165

AC XY:

1984

AN XY:

120262

show subpopulations

Gnomad AFR exome

AF:

0.00366

Gnomad AMR exome

AF:

0.00508

Gnomad ASJ exome

AF:

0.00478

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00113

Gnomad FIN exome

AF:

0.0382

Gnomad NFE exome

AF:

0.0256

Gnomad OTH exome

AF:

0.0135

GnomAD4 exome

AF:

0.0198

AC:

28660

AN:

1447558

Hom.:

360

Cov.:

AF XY:

0.0193

AC XY:

13892

AN XY:

719216

show subpopulations

Gnomad4 AFR exome

AF:

0.00342

Gnomad4 AMR exome

AF:

0.00601

Gnomad4 ASJ exome

AF:

0.00461

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00139

Gnomad4 FIN exome

AF:

0.0385

Gnomad4 NFE exome

AF:

0.0227

Gnomad4 OTH exome

AF:

0.0144

GnomAD4 genome

AF:

0.0157

AC:

2395

AN:

152288

Hom.:

Cov.:

AF XY:

0.0163

AC XY:

1210

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00419

Gnomad4 AMR

AF:

0.00849

Gnomad4 ASJ

AF:

0.00519

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00186

Gnomad4 FIN

AF:

0.0389

Gnomad4 NFE

AF:

0.0238

Gnomad4 OTH

AF:

0.00805

Alfa

AF:

0.0134

Hom.:

Bravo

AF:

0.0128

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.4

DANN

Benign

0.78

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over