19-41767097-T-C

Position:

• chr19-41767097-T-C

Variant summary

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

The NM_002483.7(CEACAM6):​c.*40+798T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,828 control chromosomes in the GnomAD database, including 21,271 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 0.52 (21271 hom., cov: 30)
• Consequence: CEACAM6 NM_002483.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM6	NM_002483.7	c.*40+798T>C		intron_variant		ENST00000199764.7
CEACAM6	XM_011526990.3	c.959-3705T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM6	ENST00000199764.7	c.*40+798T>C		intron_variant		1	NM_002483.7	P1
	ENST00000601409.1	n.384-9016A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79520 AN: 151706 Hom.: 21253 Cov.: 30

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.524 AC: 79582 AN: 151828 Hom.: 21271 Cov.: 30 AF XY: 0.523 AC XY: 38802 AN XY: 74198

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.549

Alfa AF: 0.572 Hom.: 49991

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10413359; hg19: chr19-42271006;