11-111297067-T-G

Variant names:

• chr11-111297067-T-G
• rs10891245
• ENST00000355430.5:n.1920A>C

Variant summary

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

The ENST00000355430.5(COLCA1):​n.1920A>C 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 0.265 in 167,518 control chromosomes in the GnomAD database, including 6,445 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 0.26 (5749 hom., cov: 34)
  • Exomes 𝑓: 0.30 (696 hom.)
• Consequence: COLCA1 ENST00000355430.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 8 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=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000355430.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLCA1	NR_169237.1		n.1821A>C		non_coding_transcript_exon	Exon 2 of 2
	COLCA1	NR_169241.1		n.1688A>C		non_coding_transcript_exon	Exon 2 of 2
	COLCA1	NR_169242.1		n.1724A>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLCA1	ENST00000355430.5	TSL:1	n.1920A>C		non_coding_transcript_exon	Exon 2 of 2
	COLCA1	ENST00000532918.4	TSL:1	n.1688A>C		non_coding_transcript_exon	Exon 2 of 2
	COLCA1	ENST00000540738.3	TSL:1	n.1859A>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39775 AN: 152134 Hom.: 5740 Cov.: 34

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.262

GnomAD4 exome AF: 0.295 AC: 4505 AN: 15266 Hom.: 696 Cov.: 0 AF XY: 0.295 AC XY: 2172 AN XY: 7354

African (AFR) AF: 0.0500 AC: 1 AN: 20

American (AMR) AF: 0.125 AC: 1 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.500 AC: 8 AN: 16

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.296 AC: 4346 AN: 14676

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.267 AC: 112 AN: 420

Other (OTH) AF: 0.307 AC: 35 AN: 114

GnomAD4 genome AF: 0.261 AC: 39811 AN: 152252 Hom.: 5749 Cov.: 34 AF XY: 0.265 AC XY: 19697 AN XY: 74428

African (AFR) AF: 0.148 AC: 6144 AN: 41570

American (AMR) AF: 0.273 AC: 4171 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 998 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2194 AN: 5174

South Asian (SAS) AF: 0.477 AC: 2305 AN: 4828

European-Finnish (FIN) AF: 0.289 AC: 3059 AN: 10596

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20155 AN: 67994

Other (OTH) AF: 0.268 AC: 565 AN: 2112

Alfa AF: 0.269 Hom.: 4138

Bravo AF: 0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.1
DANN	Benign	0.83
PhyloP100		0.046
Mutation Taster		=300/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10891245; hg19: chr11-111167792; COSMIC: COSV62619013;