rs4803507

Positions:

• chr19-41759642-G-A

Variant summary

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

The NM_002483.7(CEACAM6):​c.425-1607G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,034 control chromosomes in the GnomAD database, including 5,629 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 0.27 (5629 hom., cov: 32)
• Consequence: CEACAM6 NM_002483.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.579

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEACAM6	NM_002483.7	c.425-1607G>A		intron_variant		ENST00000199764.7	NP_002474.4
CEACAM6	XM_011526990.3	c.425-1607G>A		intron_variant			XP_011525292.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEACAM6	ENST00000199764.7	c.425-1607G>A		intron_variant		1	NM_002483.7	ENSP00000199764	P1
	ENST00000601409.1	n.384-1561C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40344 AN: 151916 Hom.: 5625 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.266 AC: 40383 AN: 152034 Hom.: 5629 Cov.: 32 AF XY: 0.267 AC XY: 19812 AN XY: 74304

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.263

Alfa AF: 0.290 Hom.: 1231

Bravo AF: 0.259

Asia WGS AF: 0.244 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.46

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: rs4803507; hg19: chr19-42263550;