rs7197758

Positions:

• chr16-10987225-G-A
• chr16-10987225-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):​c.1071+4234G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,786 control chromosomes in the GnomAD database, including 8,307 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 (8307 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.857

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.1071+4234G>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1071+4234G>A		intron_variant		5	NM_015226.3	A1
CLEC16A	ENST00000409552.4	c.1065+4234G>A		intron_variant		1
CLEC16A	ENST00000703130.1	c.1065+4234G>A		intron_variant				P4
CLEC16A	ENST00000494853.1	n.546+4234G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48943 AN: 151668 Hom.: 8294 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.323 AC: 48999 AN: 151786 Hom.: 8307 Cov.: 31 AF XY: 0.320 AC XY: 23738 AN XY: 74180

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.301

Alfa AF: 0.287 Hom.: 10977

Bravo AF: 0.324

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.32

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: rs7197758; hg19: chr16-11081082;