NM_015226.3:c.1071+4401C>G

Variant names:

• chr16-10987392-C-G
• rs6498142
• NM_015226.3:c.1071+4401C>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.1071+4401C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 151,986 control chromosomes in the GnomAD database, including 45,576 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 0.77 (45576 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 26 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1071+4401C>G		intron_variant	Intron 10 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1071+4401C>G		intron_variant	Intron 10 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1065+4401C>G		intron_variant	Intron 9 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1065+4401C>G		intron_variant	Intron 9 of 22			ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.546+4401C>G		intron_variant	Intron 5 of 7	3

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117014 AN: 151868 Hom.: 45545 Cov.: 31

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.770 AC: 117094 AN: 151986 Hom.: 45576 Cov.: 31 AF XY: 0.772 AC XY: 57351 AN XY: 74304

African (AFR) AF: 0.655 AC: 27114 AN: 41416

American (AMR) AF: 0.828 AC: 12637 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2601 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4658 AN: 5164

South Asian (SAS) AF: 0.776 AC: 3747 AN: 4826

European-Finnish (FIN) AF: 0.832 AC: 8786 AN: 10560

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54934 AN: 67974

Other (OTH) AF: 0.775 AC: 1635 AN: 2110

Alfa AF: 0.803 Hom.: 26558

Bravo AF: 0.769

Asia WGS AF: 0.803 AC: 2794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.29
PhyloP100		0.37
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: rs6498142; hg19: chr16-11081249;