11-111293999-G-T

Variant names:

• chr11-111293999-G-T
• rs45615536
• ENST00000355430.5:n.4988C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000355430.5(COLCA1):​n.4988C>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 ENST00000355430.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
COLCA1	NR_169237.1	n.4889C>A		non_coding_transcript_exon_variant	Exon 2 of 2
COLCA1	NR_169241.1	n.4756C>A		non_coding_transcript_exon_variant	Exon 2 of 2
COLCA1	NR_169242.1	n.4792C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLCA1	ENST00000355430.5	n.4988C>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
COLCA1	ENST00000532918.4	n.4756C>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
COLCA1	ENST00000540738.3	n.4927C>A		non_coding_transcript_exon_variant	Exon 2 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0960 AC: 19 AN: 198

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0234 AC: 971 AN: 41460

American (AMR) AF: 0.126 AC: 1922 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3472

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5186

South Asian (SAS) AF: 0.0460 AC: 221 AN: 4802

European-Finnish (FIN) AF: 0.0937 AC: 992 AN: 10590

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8631 AN: 67904

Other (OTH) AF: 0.113 AC: 238 AN: 2104

Alfa AF: 0.0982 Hom.: 455

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
PhyloP100		-0.0020
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs45615536; hg19: chr11-111164724;