rs7201845

Variant names:

• chr16-10984481-G-A
• rs7201845
• NM_015226.3:c.1071+1490G>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.1071+1490G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,238 control chromosomes in the GnomAD database, including 54,120 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 0.84 (54120 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 9 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 = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1071+1490G>A		intron_variant	Intron 10 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1071+1490G>A		intron_variant	Intron 10 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1065+1490G>A		intron_variant	Intron 9 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1065+1490G>A		intron_variant	Intron 9 of 22			ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.546+1490G>A		intron_variant	Intron 5 of 7	3

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127639 AN: 152120 Hom.: 54050 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.839 AC: 127768 AN: 152238 Hom.: 54120 Cov.: 32 AF XY: 0.840 AC XY: 62504 AN XY: 74408

African (AFR) AF: 0.956 AC: 39722 AN: 41556

American (AMR) AF: 0.834 AC: 12767 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2477 AN: 3470

East Asian (EAS) AF: 0.937 AC: 4850 AN: 5178

South Asian (SAS) AF: 0.809 AC: 3902 AN: 4826

European-Finnish (FIN) AF: 0.805 AC: 8530 AN: 10598

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52859 AN: 67994

Other (OTH) AF: 0.817 AC: 1727 AN: 2114

Alfa AF: 0.809 Hom.: 27451

Bravo AF: 0.849

Asia WGS AF: 0.861 AC: 2992 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	0.072
DANN	Benign	0.57
PhyloP100		-2.6
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: rs7201845; hg19: chr16-11078338;