rs3764577

Positions:

• chr19-41752698-A-C
• chr19-41752698-A-T

Variant summary

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

The ENST00000595740.1(CEACAM6):​c.-120+950A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,978 control chromosomes in the GnomAD database, including 11,681 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 0.39 (11681 hom., cov: 31)
• Consequence: CEACAM6 ENST00000595740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

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]

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 = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEACAM6	ENST00000595740.1	c.-120+950A>C		intron_variant		4		ENSP00000469752

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59080 AN: 151860 Hom.: 11661 Cov.: 31

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.389 AC: 59148 AN: 151978 Hom.: 11681 Cov.: 31 AF XY: 0.389 AC XY: 28912 AN XY: 74298

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.358

Alfa AF: 0.350 Hom.: 4266

Bravo AF: 0.393

Asia WGS AF: 0.341 AC: 1187 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	5.4
DANN	Benign	0.53

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: rs3764577; hg19: chr19-42256606;