rs7198004

Variant names:

• chr16-11113760-A-G
• rs7198004
• NM_015226.3:c.2117-6855A>G

Variant summary

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

The NM_015226.3(CLEC16A):​c.2117-6855A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,098 control chromosomes in the GnomAD database, including 17,737 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 0.47 (17737 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 18 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015226.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	NM_015226.3	MANE Select	c.2117-6855A>G		intron	N/A	NP_056041.1	Q2KHT3-1
	CLEC16A	NM_001410905.1		c.2111-6855A>G		intron	N/A	NP_001397834.1	A0A8V8TR67
	CLEC16A	NM_001243403.2		c.2063-6855A>G		intron	N/A	NP_001230332.1	Q2KHT3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2117-6855A>G		intron	N/A	ENSP00000387122.1	Q2KHT3-1
	CLEC16A	ENST00000409552.4	TSL:1	c.2063-6855A>G		intron	N/A	ENSP00000386495.3	Q2KHT3-2
	CLEC16A	ENST00000904405.1		c.2111-6855A>G		intron	N/A	ENSP00000574464.1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72156 AN: 151980 Hom.: 17702 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.475 AC: 72246 AN: 152098 Hom.: 17737 Cov.: 32 AF XY: 0.470 AC XY: 34949 AN XY: 74362

African (AFR) AF: 0.606 AC: 25136 AN: 41478

American (AMR) AF: 0.393 AC: 6010 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1785 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1828 AN: 5184

South Asian (SAS) AF: 0.437 AC: 2105 AN: 4818

European-Finnish (FIN) AF: 0.403 AC: 4267 AN: 10588

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29577 AN: 67944

Other (OTH) AF: 0.482 AC: 1018 AN: 2110

Alfa AF: 0.466 Hom.: 3306

Bravo AF: 0.479

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.41
PhyloP100		0.60
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: rs7198004; hg19: chr16-11207617;