rs2165538

Positions:

• chr19-44671859-C-G

Variant summary

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

The NM_001127893.3(CEACAM19):​c.-73C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0165 in 1,396,470 control chromosomes in the GnomAD database, including 1,456 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 0.058 (723 hom., cov: 32)
  • Exomes 𝑓: 0.011 (733 hom.)
• Consequence: CEACAM19 NM_001127893.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

Genes affected

CEACAM19 (HGNC:31951): (CEA cell adhesion molecule 19) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CEACAM16-AS1 (HGNC:55317): (CEACAM16, CEACAM19 and PVR antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEACAM19	NM_001127893.3	c.-73C>G		5_prime_UTR_variant	1/8	ENST00000358777.10
CEACAM19	NM_001389722.1	c.-73C>G		5_prime_UTR_variant	2/9
CEACAM19	NM_020219.5	c.-73C>G		5_prime_UTR_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM19	ENST00000358777.10	c.-73C>G		5_prime_UTR_variant	1/8	1	NM_001127893.3	A2
CEACAM16-AS1	ENST00000662585.1	n.475+27225G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0578 AC: 8789 AN: 152116 Hom.: 722 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0263

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00157

Gnomad OTH AF: 0.0459

GnomAD4 exome AF: 0.0114 AC: 14187 AN: 1244236 Hom.: 733 Cov.: 17 AF XY: 0.0120 AC XY: 7453 AN XY: 622220

Gnomad4 AFR exome AF: 0.189

Gnomad4 AMR exome AF: 0.0145

Gnomad4 ASJ exome AF: 0.0126

Gnomad4 EAS exome AF: 0.0443

Gnomad4 SAS exome AF: 0.0408

Gnomad4 FIN exome AF: 0.0342

Gnomad4 NFE exome AF: 0.000547

Gnomad4 OTH exome AF: 0.0195

GnomAD4 genome AF: 0.0578 AC: 8799 AN: 152234 Hom.: 723 Cov.: 32 AF XY: 0.0579 AC XY: 4309 AN XY: 74432

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.0262

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.0224

Gnomad4 SAS AF: 0.0379

Gnomad4 FIN AF: 0.0335

Gnomad4 NFE AF: 0.00157

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0352 Hom.: 60

Bravo AF: 0.0624

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.2
DANN	Benign	0.84

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: rs2165538; hg19: chr19-45175131;