rs7201845

chr16-10984481-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• 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/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.1071+1490G>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1071+1490G>A		intron_variant		5	NM_015226.3	A1
CLEC16A	ENST00000409552.4	c.1065+1490G>A		intron_variant		1
CLEC16A	ENST00000703130.1	c.1065+1490G>A		intron_variant				P4
CLEC16A	ENST00000494853.1	n.546+1490G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.817

Alfa AF: 0.808 Hom.: 23340

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

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: rs7201845; hg19: chr16-11078338;