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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
COLCA1	NR_169237.1 link	n.3109C>T	non_coding_transcript_exon_variant	Exon 2 of 2
COLCA1	NR_169241.1 link	n.2976C>T	non_coding_transcript_exon_variant	Exon 2 of 2
COLCA1	NR_169242.1 link	n.3012C>T	non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
COLCA1	ENST00000355430.5 link	n.3208C>T	non_coding_transcript_exon_variant	Exon 2 of 2	1
COLCA1	ENST00000532918.4 link	n.2976C>T	non_coding_transcript_exon_variant	Exon 2 of 2	1
COLCA1	ENST00000540738.3 link	n.3147C>T	non_coding_transcript_exon_variant	Exon 2 of 2	1

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 v4.3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over