chr19-42547219-A-T

Variant names:

• chr19-42547219-A-T
• rs10401935
• ENST00000594624.8:n.233+61996A>T

Variant summary

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

The ENST00000594624.8(LIPE-AS1):​n.233+61996A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,646 control chromosomes in the GnomAD database, including 20,728 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 0.48 (20728 hom., cov: 29)
• Consequence: LIPE-AS1 ENST00000594624.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 0 publications found

Genes affected

LIPE-AS1 (HGNC:48589): (LIPE antisense RNA 1)

CEACAM1 (HGNC:1814): (CEA cell adhesion molecule 1) This gene encodes a member of the carcinoembryonic antigen (CEA) gene family, which belongs to the immunoglobulin superfamily. Two subgroups of the CEA family, the CEA cell adhesion molecules and the pregnancy-specific glycoproteins, are located within a 1.2 Mb cluster on the long arm of chromosome 19. Eleven pseudogenes of the CEA cell adhesion molecule subgroup are also found in the cluster. The encoded protein was originally described in bile ducts of liver as biliary glycoprotein. Subsequently, it was found to be a cell-cell adhesion molecule detected on leukocytes, epithelia, and endothelia. The encoded protein mediates cell adhesion via homophilic as well as heterophilic binding to other proteins of the subgroup. Multiple cellular activities have been attributed to the encoded protein, including roles in the differentiation and arrangement of tissue three-dimensional structure, angiogenesis, apoptosis, tumor suppression, metastasis, and the modulation of innate and adaptive immune responses. Multiple transcript variants encoding different isoforms have been reported, but the full-length nature of all variants has not been defined. [provided by RefSeq, May 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPE-AS1	NR_073179.1	n.1451-103868A>T		intron_variant	Intron 1 of 1
LIPE-AS1	NR_073180.1	n.205+61996A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPE-AS1	ENST00000594624.8	n.233+61996A>T		intron_variant	Intron 2 of 2	1
CEACAM1	ENST00000600172.1	c.-101+13979T>A		intron_variant	Intron 1 of 2	5		ENSP00000471566.1
LIPE-AS1	ENST00000594688.1	n.1451-103868A>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.475 AC: 71933 AN: 151524 Hom.: 20672 Cov.: 29

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.475 AC: 72049 AN: 151646 Hom.: 20728 Cov.: 29 AF XY: 0.469 AC XY: 34729 AN XY: 74064

African (AFR) AF: 0.822 AC: 33931 AN: 41294

American (AMR) AF: 0.396 AC: 6044 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1223 AN: 3470

East Asian (EAS) AF: 0.151 AC: 774 AN: 5140

South Asian (SAS) AF: 0.323 AC: 1544 AN: 4782

European-Finnish (FIN) AF: 0.380 AC: 4000 AN: 10516

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23311 AN: 67878

Other (OTH) AF: 0.433 AC: 913 AN: 2110

Alfa AF: 0.420 Hom.: 1857

Bravo AF: 0.490

Asia WGS AF: 0.316 AC: 1098 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	0.39
DANN	Benign	0.69
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10401935; hg19: chr19-43051371;