chr16-11177047-C-A

Variant names:

• chr16-11177047-C-A
• rs3960630
• NM_015226.3:c.2807-1288C>A

Variant summary

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

The NM_015226.3(CLEC16A):​c.2807-1288C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,104 control chromosomes in the GnomAD database, including 4,811 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 0.25 (4811 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 12 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2807-1288C>A		intron_variant	Intron 23 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2807-1288C>A		intron_variant	Intron 23 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000703130.1	c.2801-1288C>A		intron_variant	Intron 22 of 22			ENSP00000515187.1
CLEC16A	ENST00000261657.5	c.*48-1288C>A		intron_variant	Intron 4 of 4	4		ENSP00000261657.5

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37534 AN: 151986 Hom.: 4802 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.247 AC: 37560 AN: 152104 Hom.: 4811 Cov.: 33 AF XY: 0.247 AC XY: 18377 AN XY: 74370

African (AFR) AF: 0.295 AC: 12245 AN: 41460

American (AMR) AF: 0.209 AC: 3196 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3472

East Asian (EAS) AF: 0.275 AC: 1424 AN: 5178

South Asian (SAS) AF: 0.264 AC: 1271 AN: 4822

European-Finnish (FIN) AF: 0.244 AC: 2582 AN: 10580

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15629 AN: 67982

Other (OTH) AF: 0.237 AC: 500 AN: 2112

Alfa AF: 0.229 Hom.: 7066

Bravo AF: 0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.4
DANN	Benign	0.62
PhyloP100		0.28
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: rs3960630; hg19: chr16-11270904;