ENST00000816694.1:n.159+13981G>A

Variant names:

• chr6-163401264-C-T
• rs4263561
• ENST00000816694.1:n.159+13981G>A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 2 publications found

Genes affected

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816694.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAHM	ENST00000816694.1		n.159+13981G>A		intron	N/A
	CAHM	ENST00000816695.1		n.151-7777G>A		intron	N/A
	CAHM	ENST00000816696.1		n.148-7777G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54134 AN: 152020 Hom.: 11296 Cov.: 33

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.: 33 AF XY: 0.363 AC XY: 27029 AN XY: 74388

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: 93 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28770 AN: 67988

Other (OTH) AF: 0.367 AC: 775 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.61
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4263561; hg19: chr6-163822296; COSMIC: COSV69432263;