NM_015226.3:c.1303+2090C>T

Variant names:

• chr16-11005395-C-T
• rs7192695
• NM_015226.3:c.1303+2090C>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.1303+2090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,072 control chromosomes in the GnomAD database, including 4,072 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 0.20 (4072 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1303+2090C>T		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.1303+2090C>T		intron_variant	Intron 11 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1249+2138C>T		intron_variant	Intron 10 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1297+2090C>T		intron_variant	Intron 10 of 22			ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.778+2090C>T		intron_variant	Intron 6 of 7	3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30672 AN: 151954 Hom.: 4058 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.202 AC: 30731 AN: 152072 Hom.: 4072 Cov.: 32 AF XY: 0.199 AC XY: 14811 AN XY: 74328

African (AFR) AF: 0.383 AC: 15861 AN: 41422

American (AMR) AF: 0.141 AC: 2152 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3470

East Asian (EAS) AF: 0.114 AC: 588 AN: 5176

South Asian (SAS) AF: 0.147 AC: 711 AN: 4822

European-Finnish (FIN) AF: 0.148 AC: 1562 AN: 10572

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8751 AN: 68000

Other (OTH) AF: 0.188 AC: 397 AN: 2114

Alfa AF: 0.145 Hom.: 2526

Bravo AF: 0.210

Asia WGS AF: 0.144 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.27
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: rs7192695; hg19: chr16-11099252;