chr19-44642803-T-C

Variant names:

• chr19-44642803-T-C
• rs7255066
• ENST00000590796.1:n.409-10184A>G

Variant summary

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

The ENST00000590796.1(CEACAM16-AS1):​n.409-10184A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,022 control chromosomes in the GnomAD database, including 17,761 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 0.42 (17761 hom., cov: 31)
• Consequence: CEACAM16-AS1 ENST00000590796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 48 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590796.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM16-AS1	ENST00000590796.1	TSL:5	n.409-10184A>G		intron	N/A
	CEACAM16-AS1	ENST00000662585.1		n.476-10184A>G		intron	N/A
	CEACAM16-AS1	ENST00000810360.1		n.90+923A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64403 AN: 151904 Hom.: 17716 Cov.: 31

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.424 AC: 64496 AN: 152022 Hom.: 17761 Cov.: 31 AF XY: 0.420 AC XY: 31218 AN XY: 74336

African (AFR) AF: 0.791 AC: 32797 AN: 41456

American (AMR) AF: 0.308 AC: 4703 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1039 AN: 3470

East Asian (EAS) AF: 0.457 AC: 2360 AN: 5162

South Asian (SAS) AF: 0.422 AC: 2038 AN: 4824

European-Finnish (FIN) AF: 0.231 AC: 2447 AN: 10584

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18093 AN: 67960

Other (OTH) AF: 0.380 AC: 797 AN: 2100

Alfa AF: 0.318 Hom.: 32855

Bravo AF: 0.442

Asia WGS AF: 0.457 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.014
DANN	Benign	0.45
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7255066; hg19: chr19-45146103;