rs7200786

Variant names:

• chr16-11083944-A-G
• rs7200786
• NM_015226.3:c.2116+22922A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-11083944-A-G
• chr16-11083944-A-T

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+22922A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,930 control chromosomes in the GnomAD database, including 26,535 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 0.58 (26535 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 63 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2116+22922A>G		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+22922A>G		intron_variant	Intron 19 of 23	5	NM_015226.3	ENSP00000387122.1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88276 AN: 151812 Hom.: 26483 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.582 AC: 88386 AN: 151930 Hom.: 26535 Cov.: 32 AF XY: 0.576 AC XY: 42760 AN XY: 74262

African (AFR) AF: 0.736 AC: 30511 AN: 41454

American (AMR) AF: 0.472 AC: 7206 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1984 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1745 AN: 5136

South Asian (SAS) AF: 0.580 AC: 2796 AN: 4822

European-Finnish (FIN) AF: 0.499 AC: 5253 AN: 10524

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37016 AN: 67928

Other (OTH) AF: 0.566 AC: 1193 AN: 2108

Alfa AF: 0.570 Hom.: 21423

Bravo AF: 0.583

Asia WGS AF: 0.492 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.72
PhyloP100		-0.16
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: rs7200786; hg19: chr16-11177801;