rs11669653

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ENSG00000268833 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CEACAM6	NM_002483.7	c.424+1388T>A		intron_variant		ENST00000199764.7	NP_002474.4
CEACAM6	XM_011526990.3	c.424+1388T>A		intron_variant			XP_011525292.1
LOC112268252	XR_002958447.2	n.336-266A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEACAM6	ENST00000199764.7	c.424+1388T>A		intron_variant		1	NM_002483.7	ENSP00000199764.6
ENSG00000268833	ENST00000601409.1	n.384-266A>T		intron_variant		4

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

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.352

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11669653; hg19: chr19-42262255;