chr16-11158972-C-T

Variant summary

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

The NM_015226.3(CLEC16A):​c.2642-7416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,532 control chromosomes in the GnomAD database, including 38,767 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 0.70 ( 38767 hom., cov: 30)

Consequence

CLEC16A
NM_015226.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0260
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CLEC16ANM_015226.3 linkuse as main transcriptc.2642-7416C>T intron_variant ENST00000409790.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLEC16AENST00000409790.6 linkuse as main transcriptc.2642-7416C>T intron_variant 5 NM_015226.3 A1Q2KHT3-1
ENST00000667071.1 linkuse as main transcriptn.174-3247G>A intron_variant, non_coding_transcript_variant
CLEC16AENST00000261657.5 linkuse as main transcriptc.216-7416C>T intron_variant 4
CLEC16AENST00000703130.1 linkuse as main transcriptc.2636-7416C>T intron_variant P4

Frequencies

GnomAD3 genomes
AF:
0.703
AC:
106510
AN:
151422
Hom.:
38719
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.877
Gnomad AMI
AF:
0.694
Gnomad AMR
AF:
0.579
Gnomad ASJ
AF:
0.675
Gnomad EAS
AF:
0.451
Gnomad SAS
AF:
0.761
Gnomad FIN
AF:
0.576
Gnomad MID
AF:
0.737
Gnomad NFE
AF:
0.662
Gnomad OTH
AF:
0.696
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.704
AC:
106609
AN:
151532
Hom.:
38767
Cov.:
30
AF XY:
0.697
AC XY:
51562
AN XY:
73938
show subpopulations
Gnomad4 AFR
AF:
0.878
Gnomad4 AMR
AF:
0.579
Gnomad4 ASJ
AF:
0.675
Gnomad4 EAS
AF:
0.451
Gnomad4 SAS
AF:
0.761
Gnomad4 FIN
AF:
0.576
Gnomad4 NFE
AF:
0.662
Gnomad4 OTH
AF:
0.696
Alfa
AF:
0.654
Hom.:
11834
Bravo
AF:
0.706
Asia WGS
AF:
0.615
AC:
2138
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.7
DANN
Benign
0.59

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

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

Other links and lift over

dbSNP: rs28087; hg19: chr16-11252829; API