rs12708716

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015226(CLEC16A):c.2116+24994A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152022 control chromosomes in the gnomAD Genomes database, including 10591 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 0.37 ( 10591 hom., cov: 33)

Consequence

CLEC16A
NM_015226 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260

Links

CLEC16A (HGNC:29013):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3 linkuse as main transcript	c.2116+24994A>G		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6 linkuse as main transcript	c.2116+24994A>G		intron_variant		5	NM_015226.3	A1	Q2KHT3-1

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56261

AN:

152022

Hom.:

10591

Cov.:

show subpopulations

Gnomad AFR

AF:

0.422

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.217

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.357

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.360

Gnomad OTH

AF:

0.380

Alfa

AF:

0.358

Hom.:

11855

Bravo

AF:

0.367

Asia WGS

AF:

0.345

AC:

1198

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

Cadd

Benign

2.5

Dann

Benign

0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over