16-10959067-T-C

Variant names:

• chr16-10959067-T-C
• rs7404554
• NM_015226.3:c.209+1157T>C

Variant summary

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

The NM_015226.3(CLEC16A):​c.209+1157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 150,914 control chromosomes in the GnomAD database, including 9,866 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 0.32 (9866 hom., cov: 30)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• 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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.209+1157T>C		intron_variant	Intron 2 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.209+1157T>C		intron_variant	Intron 2 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.209+1157T>C		intron_variant	Intron 2 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.209+1157T>C		intron_variant	Intron 2 of 22			ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48495 AN: 150796 Hom.: 9864 Cov.: 30

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.321 AC: 48499 AN: 150914 Hom.: 9866 Cov.: 30 AF XY: 0.328 AC XY: 24192 AN XY: 73742

African (AFR) AF: 0.0747 AC: 3046 AN: 40792

American (AMR) AF: 0.454 AC: 6908 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1012 AN: 3454

East Asian (EAS) AF: 0.588 AC: 3029 AN: 5148

South Asian (SAS) AF: 0.287 AC: 1376 AN: 4802

European-Finnish (FIN) AF: 0.479 AC: 4989 AN: 10418

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27108 AN: 67776

Other (OTH) AF: 0.324 AC: 679 AN: 2094

Alfa AF: 0.376 Hom.: 5936

Bravo AF: 0.312

Asia WGS AF: 0.402 AC: 1399 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.7
DANN	Benign	0.84
PhyloP100		-0.28
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: rs7404554; hg19: chr16-11052924;