chr16-11012201-G-A

Variant names:

• chr16-11012201-G-A
• rs11074945
• NM_015226.3:c.1304-7992G>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.1304-7992G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 152,216 control chromosomes in the GnomAD database, including 364 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 0.057 (364 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.084 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1304-7992G>A		intron_variant	Intron 11 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1304-7992G>A		intron_variant	Intron 11 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1250-7992G>A		intron_variant	Intron 10 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1298-7992G>A		intron_variant	Intron 10 of 22			ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.779-7992G>A		intron_variant	Intron 6 of 7	3

Frequencies

GnomAD3 genomes AF: 0.0566 AC: 8610 AN: 152098 Hom.: 364 Cov.: 32

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0565 AC: 8605 AN: 152216 Hom.: 364 Cov.: 32 AF XY: 0.0562 AC XY: 4180 AN XY: 74416

African (AFR) AF: 0.0137 AC: 569 AN: 41536

American (AMR) AF: 0.0431 AC: 659 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5194

South Asian (SAS) AF: 0.0812 AC: 391 AN: 4818

European-Finnish (FIN) AF: 0.0781 AC: 826 AN: 10574

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0858 AC: 5836 AN: 68010

Other (OTH) AF: 0.0488 AC: 103 AN: 2112

Alfa AF: 0.0793 Hom.: 547

Bravo AF: 0.0503

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		0.50
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: rs11074945; hg19: chr16-11106058;