rs2041670

Variant names:

• chr16-11080795-G-A
• rs2041670
• NM_015226.3:c.2116+19773G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-11080795-G-A
• chr16-11080795-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):​c.2116+19773G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,036 control chromosomes in the GnomAD database, including 12,249 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 0.39 (12249 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 34 publications found

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 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2116+19773G>A		intron_variant	Intron 19 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2116+19773G>A		intron_variant	Intron 19 of 23	5	NM_015226.3	ENSP00000387122.1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58546 AN: 151916 Hom.: 12211 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.376

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.386 AC: 58640 AN: 152036 Hom.: 12249 Cov.: 33 AF XY: 0.383 AC XY: 28429 AN XY: 74302

African (AFR) AF: 0.556 AC: 23088 AN: 41498

American (AMR) AF: 0.296 AC: 4527 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1095 AN: 5174

South Asian (SAS) AF: 0.380 AC: 1832 AN: 4826

European-Finnish (FIN) AF: 0.330 AC: 3479 AN: 10548

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22144 AN: 67940

Other (OTH) AF: 0.379 AC: 798 AN: 2106

Alfa AF: 0.340 Hom.: 15443

Bravo AF: 0.388

Asia WGS AF: 0.339 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.77
DANN	Benign	0.34
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2041670; hg19: chr16-11174652;