dbSNP rs12296076: COLCA1:n.3208C>T (chr11-111295779-G-A) – 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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45

Publications

8 publications found

Variant links:

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:

Genome browser will be placed here

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=-0.94).

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

Gene	Transcript	HGVSc	Effect	Exon Rank
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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
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.:

show subpopulations

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.:

AF XY:

0.680

AC XY:

4433

AN XY:

6516

show subpopulations

African (AFR)

AF:

0.580

AC:

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:

AN:

European-Non Finnish (NFE)

AF:

0.655

AC:

4965

AN:

7582

Other (OTH)

AF:

0.665

AC:

383

AN:

576

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

113

226

340

453

566

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

136

204

272

340

<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:

0.686

AC:

104168

AN:

151882

Hom.:

35934

Cov.:

AF XY:

0.692

AC XY:

51329

AN XY:

74228

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1672

3344

5015

6687

8359

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

824

1648

2472

3296

4120

<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:

0.691

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

(source)

DANN

Benign

0.23

PhyloP100

-1.4

Mutation Taster

=100/0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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