rs2701

Variant names:

• chr19-41771194-G-A
• rs2701
• NM_002483.7:c.*433G>A

Variant summary

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

The NM_002483.7(CEACAM6):​c.*433G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,056 control chromosomes in the GnomAD database, including 18,121 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 0.46 (18121 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CEACAM6 NM_002483.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 16 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002483.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM6	NM_002483.7	MANE Select	c.*433G>A		3_prime_UTR	Exon 6 of 6	NP_002474.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM6	ENST00000199764.7	TSL:1 MANE Select	c.*433G>A		3_prime_UTR	Exon 6 of 6	ENSP00000199764.6
	ENSG00000268833	ENST00000601409.1	TSL:4	n.384-13113C>T		intron	N/A
	ENSG00000268833	ENST00000819470.1		n.111-13113C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69462 AN: 151938 Hom.: 18123 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.509

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.457 AC: 69463 AN: 152056 Hom.: 18121 Cov.: 32 AF XY: 0.458 AC XY: 34027 AN XY: 74306

African (AFR) AF: 0.191 AC: 7925 AN: 41496

American (AMR) AF: 0.491 AC: 7504 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2105 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2191 AN: 5174

South Asian (SAS) AF: 0.588 AC: 2840 AN: 4826

European-Finnish (FIN) AF: 0.534 AC: 5623 AN: 10526

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.580 AC: 39394 AN: 67970

Other (OTH) AF: 0.504 AC: 1062 AN: 2106

Alfa AF: 0.513 Hom.: 11133

Bravo AF: 0.438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2701; hg19: chr19-42275099;