Genetic Variant CAHM:n.159+13981G>A (chr6-163401264-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000816694.1(CAHM):n.159+13981G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,140 control chromosomes in the GnomAD database, including 11,301 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 0.36 ( 11301 hom., cov: 33)

Consequence

CAHM
ENST00000816694.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.139

Publications

2 publications found

Variant links:

COSMIC-nc: COSV69432263

Genes affected

CAHM (HGNC:42860): (colon adenocarcinoma hypermethylated)

CAHM 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
CAHM	ENST00000816694.1 link	n.159+13981G>A	intron_variant	Intron 1 of 1
CAHM	ENST00000816695.1 link	n.151-7777G>A	intron_variant	Intron 1 of 2
CAHM	ENST00000816696.1 link	n.148-7777G>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.356

AC:

54134

AN:

152020

Hom.:

11296

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.402

Gnomad AMR

AF:

0.330

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.714

Gnomad SAS

AF:

0.485

Gnomad FIN

AF:

0.513

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.423

Gnomad OTH

AF:

0.365

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.356

AC:

54152

AN:

152140

Hom.:

11301

Cov.:

AF XY:

0.363

AC XY:

27029

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.150

AC:

6247

AN:

41518

American (AMR)

AF:

0.330

AC:

5044

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.405

AC:

1407

AN:

3470

East Asian (EAS)

AF:

0.714

AC:

3693

AN:

5172

South Asian (SAS)

AF:

0.484

AC:

2332

AN:

4820

European-Finnish (FIN)

AF:

0.513

AC:

5424

AN:

10568

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.423

AC:

28770

AN:

67988

Other (OTH)

AF:

0.367

AC:

775

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1704

3407

5111

6814

8518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

540

1080

1620

2160

2700

<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:

0.383

Hom.:

5645

Bravo

AF:

0.331

Asia WGS

AF:

0.574

AC:

1994

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.77

(source)

DANN

Benign

0.61

PhyloP100

-0.14

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over