rs3795018

Positions:

• chr19-41757812-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.424+853G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,002 control chromosomes in the GnomAD database, including 8,146 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 0.32 (8145 hom., cov: 32)
  • Exomes 𝑓: 0.23 (1 hom.)
• Consequence: CEACAM6 NM_002483.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.515

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]

LOC112268252 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM6	NM_002483.7	c.424+853G>A		intron_variant		ENST00000199764.7
LOC112268252	XR_002958447.2	n.605C>T		non_coding_transcript_exon_variant	2/2
CEACAM6	XM_011526990.3	c.424+853G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM6	ENST00000199764.7	c.424+853G>A		intron_variant		1	NM_002483.7	P1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48947 AN: 151858 Hom.: 8132 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.304

GnomAD4 exome AF: 0.231 AC: 6 AN: 26 Hom.: 1 AF XY: 0.250 AC XY: 5 AN XY: 20

Gnomad4 NFE exome AF: 0.231

GnomAD4 genome AF: 0.322 AC: 49002 AN: 151976 Hom.: 8145 Cov.: 32 AF XY: 0.329 AC XY: 24435 AN XY: 74268

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.311

Alfa AF: 0.316 Hom.: 1395

Bravo AF: 0.316

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.5
DANN	Benign	0.75

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: rs3795018; hg19: chr19-42261720;