rs2701

chr19-41771194-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.*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

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 = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM6	NM_002483.7	c.*433G>A		3_prime_UTR_variant	6/6	ENST00000199764.7
CEACAM6	XM_011526990.3	c.*376G>A		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM6	ENST00000199764.7	c.*433G>A		3_prime_UTR_variant	6/6	1	NM_002483.7	P1
	ENST00000601409.1	n.384-13113C>T		intron_variant, non_coding_transcript_variant		4

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

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

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.504

Alfa AF: 0.512 Hom.: 9545

Bravo AF: 0.438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2701; hg19: chr19-42275099;