19-44672044-T-C

Position:

• chr19-44672044-T-C

Variant summary

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

The NM_001127893.3(CEACAM19):​c.55+58T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 1,412,662 control chromosomes in the GnomAD database, including 615 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 0.035 (234 hom., cov: 32)
  • Exomes 𝑓: 0.0092 (381 hom.)
• Consequence: CEACAM19 NM_001127893.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0995 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEACAM19	NM_001127893.3	c.55+58T>C		intron_variant		ENST00000358777.10	NP_001121365.1
CEACAM19	NM_001389722.1	c.55+58T>C		intron_variant			NP_001376651.1
CEACAM19	NM_020219.5	c.55+58T>C		intron_variant			NP_064604.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEACAM19	ENST00000358777.10	c.55+58T>C		intron_variant		1	NM_001127893.3	ENSP00000351627	A2
CEACAM16-AS1	ENST00000662585.1	n.475+27040A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0354 AC: 5378 AN: 152034 Hom.: 234 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.0337

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00141

Gnomad OTH AF: 0.0253

GnomAD4 exome AF: 0.00924 AC: 11641 AN: 1260510 Hom.: 381 AF XY: 0.0101 AC XY: 6375 AN XY: 630196

Gnomad4 AFR exome AF: 0.107

Gnomad4 AMR exome AF: 0.0100

Gnomad4 ASJ exome AF: 0.0128

Gnomad4 EAS exome AF: 0.0430

Gnomad4 SAS exome AF: 0.0408

Gnomad4 FIN exome AF: 0.0341

Gnomad4 NFE exome AF: 0.000502

Gnomad4 OTH exome AF: 0.0151

GnomAD4 genome AF: 0.0354 AC: 5383 AN: 152152 Hom.: 234 Cov.: 32 AF XY: 0.0365 AC XY: 2714 AN XY: 74392

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0202

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.0230

Gnomad4 SAS AF: 0.0373

Gnomad4 FIN AF: 0.0337

Gnomad4 NFE AF: 0.00141

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.00813 Hom.: 41

Bravo AF: 0.0373

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.60

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: rs1550551; hg19: chr19-45175316; COSMIC: COSV62551960; COSMIC: COSV62551960;