19-41767097-T-C

Variant names:

• chr19-41767097-T-C
• rs10413359
• NM_002483.7:c.*40+798T>C

Variant summary

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

The NM_002483.7(CEACAM6):​c.*40+798T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,828 control chromosomes in the GnomAD database, including 21,271 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 0.52 (21271 hom., cov: 30)
• Consequence: CEACAM6 NM_002483.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• Publications: 9 publications found

Genes affected

CEACAM6 (HGNC:1818): (CEA cell adhesion molecule 6) This gene encodes a protein that belongs to the carcinoembryonic antigen (CEA) family whose members are glycosyl phosphatidyl inositol (GPI) anchored cell surface glycoproteins. Members of this family play a role in cell adhesion and are widely used as tumor markers in serum immunoassay determinations of carcinoma. This gene affects the sensitivity of tumor cells to adenovirus infection. The protein encoded by this gene acts as a receptor for adherent-invasive E. coli adhesion to the surface of ileal epithelial cells in patients with Crohn's disease. This gene is clustered with genes and pseudogenes of the cell adhesion molecules subgroup of the CEA family on chromosome 19. [provided by RefSeq, Apr 2014]

CEACAM6 Gene-Disease associations (from GenCC):

• cystic fibrosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000268833 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEACAM6	NM_002483.7	c.*40+798T>C		intron_variant	Intron 5 of 5	ENST00000199764.7	NP_002474.4
CEACAM6	XM_011526990.3	c.959-3705T>C		intron_variant	Intron 4 of 4		XP_011525292.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAM6	ENST00000199764.7	c.*40+798T>C		intron_variant	Intron 5 of 5	1	NM_002483.7	ENSP00000199764.6
ENSG00000268833	ENST00000601409.1	n.384-9016A>G		intron_variant	Intron 1 of 1	4
ENSG00000268833	ENST00000819470.1	n.111-9016A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79520 AN: 151706 Hom.: 21253 Cov.: 30

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.524 AC: 79582 AN: 151828 Hom.: 21271 Cov.: 30 AF XY: 0.523 AC XY: 38802 AN XY: 74198

African (AFR) AF: 0.424 AC: 17546 AN: 41394

American (AMR) AF: 0.516 AC: 7865 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3472

East Asian (EAS) AF: 0.425 AC: 2198 AN: 5176

South Asian (SAS) AF: 0.591 AC: 2844 AN: 4814

European-Finnish (FIN) AF: 0.533 AC: 5605 AN: 10512

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.581 AC: 39439 AN: 67904

Other (OTH) AF: 0.549 AC: 1153 AN: 2100

Alfa AF: 0.566 Hom.: 102600

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10413359; hg19: chr19-42271006;