rs11669653

Variant names:

• chr19-41758347-T-A
• rs11669653
• NM_002483.7:c.424+1388T>A

Your query was ambiguous. Multiple possible variants found:

• chr19-41758347-T-A
• chr19-41758347-T-G

Variant summary

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

The NM_002483.7(CEACAM6):​c.424+1388T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,844 control chromosomes in the GnomAD database, including 11,569 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 0.38 (11569 hom., cov: 31)
• Consequence: CEACAM6 NM_002483.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 6 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEACAM6	NM_002483.7	c.424+1388T>A		intron_variant	Intron 2 of 5	ENST00000199764.7	NP_002474.4
CEACAM6	XM_011526990.3	c.424+1388T>A		intron_variant	Intron 2 of 4		XP_011525292.1
LOC112268252	XR_002958447.2	n.336-266A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAM6	ENST00000199764.7	c.424+1388T>A		intron_variant	Intron 2 of 5	1	NM_002483.7	ENSP00000199764.6
ENSG00000268833	ENST00000601409.1	n.384-266A>T		intron_variant	Intron 1 of 1	4
ENSG00000268833	ENST00000819470.1	n.111-266A>T		intron_variant	Intron 1 of 1
ENSG00000268833	ENST00000819471.1	n.346-266A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57435 AN: 151726 Hom.: 11540 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.379 AC: 57528 AN: 151844 Hom.: 11569 Cov.: 31 AF XY: 0.385 AC XY: 28563 AN XY: 74208

African (AFR) AF: 0.509 AC: 21071 AN: 41384

American (AMR) AF: 0.323 AC: 4934 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3468

East Asian (EAS) AF: 0.514 AC: 2656 AN: 5164

South Asian (SAS) AF: 0.493 AC: 2369 AN: 4810

European-Finnish (FIN) AF: 0.369 AC: 3879 AN: 10518

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20392 AN: 67932

Other (OTH) AF: 0.352 AC: 741 AN: 2108

Alfa AF: 0.346 Hom.: 1213

Bravo AF: 0.380

Asia WGS AF: 0.521 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.76
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11669653; hg19: chr19-42262255;