11-111293999-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_169237.1(COLCA1):n.4889C>A 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 0.0928 in 152,204 control chromosomes in the GnomAD database, including 919 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 0.093 (918 hom., cov: 33)
  • Exomes 𝑓: 0.096 (1 hom.)
• Consequence: COLCA1 NR_169237.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COLCA1	NR_169237.1	n.4889C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COLCA1	ENST00000620864.1	n.4886C>A		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.0929 AC: 14105 AN: 151888 Hom.: 919 Cov.: 33

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.114

GnomAD4 exome AF: 0.0960 AC: 19 AN: 198 Hom.: 1 Cov.: 0 AF XY: 0.0917 AC XY: 11 AN XY: 120

Gnomad4 FIN exome AF: 0.0960

GnomAD4 genome AF: 0.0927 AC: 14098 AN: 152006 Hom.: 918 Cov.: 33 AF XY: 0.0911 AC XY: 6769 AN XY: 74330

Gnomad4 AFR AF: 0.0234

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.0937

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0951 Hom.: 277

Bravo AF: 0.0937

Asia WGS AF: 0.0260 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.32
Dann	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs45615536; hg19: chr11-111164724;