rs16892015

Variant summary

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

The NM_006438.5(COLEC10):​c.293-1519A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0322 in 152,164 control chromosomes in the GnomAD database, including 120 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 0.032 ( 120 hom., cov: 32)

Consequence

COLEC10
NM_006438.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.647
Variant links:
Genes affected
COLEC10 (HGNC:2220): (collectin subfamily member 10) This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. The other members of this family are secreted proteins and bind to carbohydrate antigens on microorganisms facilitating their recognition and removal. This gene product is a cytosolic protein, a characteristic that suggests that it may have different biological functions than other C-lectins. [provided by RefSeq, Jul 2008]

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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=-0.8).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COLEC10NM_006438.5 linkuse as main transcriptc.293-1519A>C intron_variant ENST00000332843.3
COLEC10NM_001324095.2 linkuse as main transcriptc.86-1519A>C intron_variant
COLEC10XM_005250756.4 linkuse as main transcriptc.86-1519A>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COLEC10ENST00000332843.3 linkuse as main transcriptc.293-1519A>C intron_variant 1 NM_006438.5 P1
COLEC10ENST00000521788.1 linkuse as main transcriptn.380-1519A>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0322
AC:
4892
AN:
152044
Hom.:
120
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0439
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0224
Gnomad ASJ
AF:
0.0671
Gnomad EAS
AF:
0.0641
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.0226
Gnomad MID
AF:
0.0669
Gnomad NFE
AF:
0.0191
Gnomad OTH
AF:
0.0411
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0322
AC:
4904
AN:
152164
Hom.:
120
Cov.:
32
AF XY:
0.0349
AC XY:
2596
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.0441
Gnomad4 AMR
AF:
0.0223
Gnomad4 ASJ
AF:
0.0671
Gnomad4 EAS
AF:
0.0644
Gnomad4 SAS
AF:
0.109
Gnomad4 FIN
AF:
0.0226
Gnomad4 NFE
AF:
0.0191
Gnomad4 OTH
AF:
0.0402
Alfa
AF:
0.0260
Hom.:
13
Bravo
AF:
0.0317
Asia WGS
AF:
0.0750
AC:
262
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
3.8
DANN
Benign
0.25

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: rs16892015; hg19: chr8-120113068; API