chr16-10997704-G-T

Position:

• chr16-10997704-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1072-5370G>T		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1072-5370G>T		intron_variant		5	NM_015226.3	ENSP00000387122	A1
CLEC16A	ENST00000409552.4	c.1066-5370G>T		intron_variant		1		ENSP00000386495
CLEC16A	ENST00000703130.1	c.1066-5370G>T		intron_variant				ENSP00000515187	P4
CLEC16A	ENST00000494853.1	n.547-5370G>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.660

Alfa AF: 0.614 Hom.: 7237

Bravo AF: 0.676

Asia WGS AF: 0.592 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	14
DANN	Benign	0.92

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

Publications

LitVar

Other links and lift over

dbSNP: rs8055544; hg19: chr16-11091561;