rs10415946

Variant names:

• chr19-41755151-A-G
• rs10415946
• ENST00000435837.2:c.65-1449A>G

Variant summary

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

The ENST00000435837.2(ENSG00000267881):​c.65-1449A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,986 control chromosomes in the GnomAD database, including 11,555 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 (11555 hom., cov: 31)
• Consequence: ENSG00000267881 ENST00000435837.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

ENSG00000267881 (HGNC:):

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267881	ENST00000435837.2	c.65-1449A>G		intron_variant	Intron 1 of 1	3		ENSP00000469926.1
CEACAM6	ENST00000595740.1	c.-119-369A>G		intron_variant	Intron 2 of 3	4		ENSP00000469752.1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58815 AN: 151868 Hom.: 11540 Cov.: 31

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.387 AC: 58874 AN: 151986 Hom.: 11555 Cov.: 31 AF XY: 0.387 AC XY: 28782 AN XY: 74290

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.360

Alfa AF: 0.368 Hom.: 10028

Bravo AF: 0.390

Asia WGS AF: 0.340 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.34

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: rs10415946; hg19: chr19-42259059;