16-11158972-C-T

Variant names:

• chr16-11158972-C-T
• rs28087
• NM_015226.3:c.2642-7416C>T

Variant summary

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

The NM_015226.3(CLEC16A):​c.2642-7416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,532 control chromosomes in the GnomAD database, including 38,767 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 0.70 (38767 hom., cov: 30)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 8 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)

ENSG00000287121 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2642-7416C>T		intron_variant	Intron 22 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2642-7416C>T		intron_variant	Intron 22 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000703130.1	c.2636-7416C>T		intron_variant	Intron 21 of 22			ENSP00000515187.1
CLEC16A	ENST00000261657.5	c.215-7416C>T		intron_variant	Intron 2 of 4	4		ENSP00000261657.5
ENSG00000287121	ENST00000667071.1	n.174-3247G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106510 AN: 151422 Hom.: 38719 Cov.: 30

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.704 AC: 106609 AN: 151532 Hom.: 38767 Cov.: 30 AF XY: 0.697 AC XY: 51562 AN XY: 73938

African (AFR) AF: 0.878 AC: 36317 AN: 41384

American (AMR) AF: 0.579 AC: 8810 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2341 AN: 3468

East Asian (EAS) AF: 0.451 AC: 2322 AN: 5150

South Asian (SAS) AF: 0.761 AC: 3664 AN: 4814

European-Finnish (FIN) AF: 0.576 AC: 5923 AN: 10280

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44916 AN: 67898

Other (OTH) AF: 0.696 AC: 1465 AN: 2104

Alfa AF: 0.651 Hom.: 18220

Bravo AF: 0.706

Asia WGS AF: 0.615 AC: 2138 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		0.026
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: rs28087; hg19: chr16-11252829;