rs12296076

Variant summary

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

The NR_169237.1(COLCA1):​n.3109C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 164,274 control chromosomes in the GnomAD database, including 38,920 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 0.69 ( 35934 hom., cov: 30)
Exomes 𝑓: 0.68 ( 2986 hom. )

Consequence

COLCA1
NR_169237.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45
Variant links:
Genes affected
COLCA1 (HGNC:33789): (colorectal cancer associated 1) This gene encodes a transmembrane protein that localizes to granular structures, including crystalloid eosinophilic granules and other granular organelles. This gene, along with an overlapping opposite strand gene, has been implicated as a susceptibility locus for colorectal cancer. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Nov 2014]

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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=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COLCA1NR_169237.1 linkuse as main transcriptn.3109C>T non_coding_transcript_exon_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COLCA1ENST00000620864.1 linkuse as main transcriptn.3106C>T non_coding_transcript_exon_variant 2/21

Frequencies

GnomAD3 genomes
AF:
0.686
AC:
104080
AN:
151768
Hom.:
35897
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.628
Gnomad AMI
AF:
0.548
Gnomad AMR
AF:
0.757
Gnomad ASJ
AF:
0.719
Gnomad EAS
AF:
0.591
Gnomad SAS
AF:
0.819
Gnomad FIN
AF:
0.767
Gnomad MID
AF:
0.785
Gnomad NFE
AF:
0.690
Gnomad OTH
AF:
0.688
GnomAD4 exome
AF:
0.679
AC:
8412
AN:
12392
Hom.:
2986
Cov.:
0
AF XY:
0.680
AC XY:
4433
AN XY:
6516
show subpopulations
Gnomad4 AFR exome
AF:
0.580
Gnomad4 AMR exome
AF:
0.738
Gnomad4 ASJ exome
AF:
0.605
Gnomad4 EAS exome
AF:
0.530
Gnomad4 SAS exome
AF:
0.805
Gnomad4 FIN exome
AF:
0.743
Gnomad4 NFE exome
AF:
0.655
Gnomad4 OTH exome
AF:
0.665
GnomAD4 genome
AF:
0.686
AC:
104168
AN:
151882
Hom.:
35934
Cov.:
30
AF XY:
0.692
AC XY:
51329
AN XY:
74228
show subpopulations
Gnomad4 AFR
AF:
0.628
Gnomad4 AMR
AF:
0.757
Gnomad4 ASJ
AF:
0.719
Gnomad4 EAS
AF:
0.591
Gnomad4 SAS
AF:
0.819
Gnomad4 FIN
AF:
0.767
Gnomad4 NFE
AF:
0.690
Gnomad4 OTH
AF:
0.692
Alfa
AF:
0.695
Hom.:
12328
Bravo
AF:
0.677
Asia WGS
AF:
0.752
AC:
2614
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.065
DANN
Benign
0.23

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: rs12296076; hg19: chr11-111166504; API