ENST00000355430.5:n.3208C>T

Variant names:

• chr11-111295779-G-A
• rs12296076
• ENST00000355430.5:n.3208C>T

Variant summary

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

The ENST00000355430.5(COLCA1):​n.3208C>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 ENST00000355430.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 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.3109C>T		non_coding_transcript_exon	Exon 2 of 2
	COLCA1	NR_169241.1		n.2976C>T		non_coding_transcript_exon	Exon 2 of 2
	COLCA1	NR_169242.1		n.3012C>T		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.3208C>T		non_coding_transcript_exon	Exon 2 of 2
	COLCA1	ENST00000532918.4	TSL:1	n.2976C>T		non_coding_transcript_exon	Exon 2 of 2
	COLCA1	ENST00000540738.3	TSL:1	n.3147C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104080 AN: 151768 Hom.: 35897 Cov.: 30

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

African (AFR) AF: 0.580 AC: 94 AN: 162

American (AMR) AF: 0.738 AC: 1234 AN: 1672

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 115 AN: 190

East Asian (EAS) AF: 0.530 AC: 249 AN: 470

South Asian (SAS) AF: 0.805 AC: 1070 AN: 1330

European-Finnish (FIN) AF: 0.743 AC: 281 AN: 378

Middle Eastern (MID) AF: 0.656 AC: 21 AN: 32

European-Non Finnish (NFE) AF: 0.655 AC: 4965 AN: 7582

Other (OTH) AF: 0.665 AC: 383 AN: 576

GnomAD4 genome AF: 0.686 AC: 104168 AN: 151882 Hom.: 35934 Cov.: 30 AF XY: 0.692 AC XY: 51329 AN XY: 74228

African (AFR) AF: 0.628 AC: 25988 AN: 41372

American (AMR) AF: 0.757 AC: 11567 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2489 AN: 3464

East Asian (EAS) AF: 0.591 AC: 3045 AN: 5154

South Asian (SAS) AF: 0.819 AC: 3944 AN: 4816

European-Finnish (FIN) AF: 0.767 AC: 8091 AN: 10548

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46852 AN: 67944

Other (OTH) AF: 0.692 AC: 1462 AN: 2112

Alfa AF: 0.691 Hom.: 25699

Bravo AF: 0.677

Asia WGS AF: 0.752 AC: 2614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.065
DANN	Benign	0.23
PhyloP100		-1.4
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: rs12296076; hg19: chr11-111166504;