rs7198004

Positions:

• chr16-11113760-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2117-6855A>G		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2117-6855A>G		intron_variant		5	NM_015226.3	ENSP00000387122	A1

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

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.482

Alfa AF: 0.462 Hom.: 3150

Bravo AF: 0.479

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.41

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

Publications

LitVar

Other links and lift over

dbSNP: rs7198004; hg19: chr16-11207617;