16-10997704-G-T

Variant names:

• chr16-10997704-G-T
• rs8055544
• NM_015226.3:c.1072-5370G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_015226.3(CLEC16A):​c.1072-5370G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,100 control chromosomes in the GnomAD database, including 36,017 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 0.67 (36017 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• 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)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015226.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	NM_015226.3	MANE Select	c.1072-5370G>T		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.1066-5370G>T		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.1066-5370G>T		intron	N/A	NP_001230332.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.1072-5370G>T		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.1066-5370G>T		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.1066-5370G>T		intron	N/A	ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101346 AN: 151982 Hom.: 35960 Cov.: 32

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.667 AC: 101461 AN: 152100 Hom.: 36017 Cov.: 32 AF XY: 0.660 AC XY: 49067 AN XY: 74370

African (AFR) AF: 0.920 AC: 38201 AN: 41544

American (AMR) AF: 0.539 AC: 8247 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2247 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2140 AN: 5164

South Asian (SAS) AF: 0.708 AC: 3419 AN: 4832

European-Finnish (FIN) AF: 0.500 AC: 5266 AN: 10536

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39718 AN: 67954

Other (OTH) AF: 0.660 AC: 1393 AN: 2112

Alfa AF: 0.632 Hom.: 8781

Bravo AF: 0.676

Asia WGS AF: 0.592 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	14
DANN	Benign	0.92
PhyloP100		0.44
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: rs8055544; hg19: chr16-11091561;