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GeneBe

8-119089747-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_006438.5(COLEC10):c.216G>A(p.Pro72=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,612,090 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0060 ( 9 hom., cov: 33)
Exomes 𝑓: 0.00063 ( 8 hom. )

Consequence

COLEC10
NM_006438.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.92
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 8-119089747-G-A is Benign according to our data. Variant chr8-119089747-G-A is described in ClinVar as [Benign]. Clinvar id is 783530.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-3.92 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00603 (919/152298) while in subpopulation AFR AF= 0.0213 (885/41570). AF 95% confidence interval is 0.0201. There are 9 homozygotes in gnomad4. There are 416 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COLEC10NM_006438.5 linkuse as main transcriptc.216G>A p.Pro72= synonymous_variant 2/6 ENST00000332843.3
COLEC10NM_001324095.2 linkuse as main transcriptc.9G>A p.Pro3= synonymous_variant 4/8
COLEC10XM_005250756.4 linkuse as main transcriptc.9G>A p.Pro3= synonymous_variant 2/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COLEC10ENST00000332843.3 linkuse as main transcriptc.216G>A p.Pro72= synonymous_variant 2/61 NM_006438.5 P1
COLEC10ENST00000521788.1 linkuse as main transcriptn.303G>A non_coding_transcript_exon_variant 3/73

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00603
AC:
918
AN:
152180
Hom.:
9
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0213
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00144
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000735
Gnomad OTH
AF:
0.00335
GnomAD3 exomes
AF:
0.00156
AC:
392
AN:
250592
Hom.:
5
AF XY:
0.00126
AC XY:
171
AN XY:
135460
show subpopulations
Gnomad AFR exome
AF:
0.0217
Gnomad AMR exome
AF:
0.000696
Gnomad ASJ exome
AF:
0.0000994
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000530
Gnomad OTH exome
AF:
0.000820
GnomAD4 exome
AF:
0.000627
AC:
915
AN:
1459792
Hom.:
8
Cov.:
29
AF XY:
0.000529
AC XY:
384
AN XY:
726274
show subpopulations
Gnomad4 AFR exome
AF:
0.0235
Gnomad4 AMR exome
AF:
0.000806
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000696
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000207
Gnomad4 OTH exome
AF:
0.00105
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00603
AC:
919
AN:
152298
Hom.:
9
Cov.:
33
AF XY:
0.00559
AC XY:
416
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.0213
Gnomad4 AMR
AF:
0.00144
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.00230
Hom.:
1
Bravo
AF:
0.00691
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.000164
EpiControl
AF:
0.0000594

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.086
Dann
Benign
0.37

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: rs116835812; hg19: chr8-120101986; COSMIC: COSV60521453; API