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GeneBe

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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260

Links

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
CLEC16ANM_015226.3 linkuse as main transcriptc.2116+24994A>G intron_variant ENST00000409790.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLEC16AENST00000409790.6 linkuse as main transcriptc.2116+24994A>G intron_variant 5 NM_015226.3 A1Q2KHT3-1

Frequencies

GnomAD3 genomes
AF:
0.370
AC:
56261
AN:
152022
Hom.:
10591
Cov.:
33
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.

Other links and lift over

dbSNP: rs12708716; hg19: chr16-11179873;