rs4803508

chr19-41760741-G-Achr19-41760741-G-Cchr19-41760741-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002483.7(CEACAM6):c.425-508G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,082 control chromosomes in the GnomAD database, including 22,467 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 0.51 (22467 hom., cov: 32)
• Consequence: CEACAM6 NM_002483.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM6	NM_002483.7	c.425-508G>A		intron_variant		ENST00000199764.7
CEACAM6	XM_011526990.3	c.425-508G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM6	ENST00000199764.7	c.425-508G>A		intron_variant		1	NM_002483.7	P1
	ENST00000601409.1	n.384-2660C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77878 AN: 151964 Hom.: 22407 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.513 AC: 77998 AN: 152082 Hom.: 22467 Cov.: 32 AF XY: 0.511 AC XY: 37990 AN XY: 74316

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.470

Alfa AF: 0.403 Hom.: 16552

Bravo AF: 0.537

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.79
Dann	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs4803508; hg19: chr19-42264649;