Genetic Variant COLCA1:n.1920A>C (chr11-111297067-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0460

Publications

8 publications found

Variant links:

COSMIC-nc: COSV62619013

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]

COLCA1 links:

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new If you want to explore the variant's impact on the transcript ENST00000355430.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Gene	Transcript	HGVSc	Effect	Exon Rank
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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
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.:

show subpopulations

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.:

AF XY:

0.295

AC XY:

2172

AN XY:

7354

show subpopulations

African (AFR)

AF:

0.0500

AC:

AN:

American (AMR)

AF:

0.125

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.296

AC:

4346

AN:

14676

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.267

AC:

112

AN:

420

Other (OTH)

AF:

0.307

AC:

AN:

114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

162

325

487

650

812

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.261

AC:

39811

AN:

152252

Hom.:

5749

Cov.:

AF XY:

0.265

AC XY:

19697

AN XY:

74428

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1526

3052

4579

6105

7631

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.83

PhyloP100

0.046

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over