chr6-163410655-G-A

Variant names:

• chr6-163410655-G-A
• rs3904720
• ENST00000816694.1:n.159+4590C>T

Variant summary

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

The ENST00000816694.1(CAHM):​n.159+4590C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,014 control chromosomes in the GnomAD database, including 5,106 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 0.24 (5106 hom., cov: 32)
• Consequence: CAHM ENST00000816694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709
• Publications: 1 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=-0.52).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.352 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+4590C>T		intron	N/A
	CAHM	ENST00000816695.1		n.150+4590C>T		intron	N/A
	CAHM	ENST00000816696.1		n.147+4590C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36214 AN: 151896 Hom.: 5101 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.238 AC: 36250 AN: 152014 Hom.: 5106 Cov.: 32 AF XY: 0.239 AC XY: 17747 AN XY: 74294

African (AFR) AF: 0.357 AC: 14797 AN: 41424

American (AMR) AF: 0.359 AC: 5488 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1215 AN: 5176

South Asian (SAS) AF: 0.190 AC: 913 AN: 4808

European-Finnish (FIN) AF: 0.138 AC: 1462 AN: 10560

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.162 AC: 11030 AN: 67980

Other (OTH) AF: 0.237 AC: 501 AN: 2114

Alfa AF: 0.229 Hom.: 773

Bravo AF: 0.260

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	14
DANN	Benign	0.78
PhyloP100		0.71

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.

Other links and lift over

dbSNP: rs3904720;

hg19: chr6-163831687;