chr16-11020335-C-T

Position:

• chr16-11020335-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

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 (HGNC:):

ACMG classification

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	c.1436+10C>T		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1436+10C>T		intron_variant		5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1382+10C>T		intron_variant		1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1430+10C>T		intron_variant				ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.911+10C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0157 AC: 2395 AN: 152170 Hom.: 33 Cov.: 33

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.: 43 AF XY: 0.0165 AC XY: 1984 AN XY: 120262

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.: 31 AF XY: 0.0193 AC XY: 13892 AN XY: 719216

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.: 33 Cov.: 33 AF XY: 0.0163 AC XY: 1210 AN XY: 74456

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.: 7

Bravo AF: 0.0128

Asia WGS AF: 0.000866 AC: 3 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

Other links and lift over

dbSNP: rs72650660; hg19: chr16-11114192;