19-44719328-T-G

Variant names:

• chr19-44719328-T-G
• rs4802234
• ENST00000657348.2:n.354-3245A>C

Variant summary

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

The ENST00000657348.2(CEACAM16-AS1):​n.354-3245A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,888 control chromosomes in the GnomAD database, including 25,131 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 0.57 (25131 hom., cov: 30)
• Consequence: CEACAM16-AS1 ENST00000657348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657348.2. 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
	CEACAM16-AS1	NR_186814.1		n.349-3245A>C		intron	N/A
	CEACAM16-AS1	NR_186815.1		n.347+5509A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEACAM16-AS1	ENST00000657348.2		n.354-3245A>C		intron	N/A
	CEACAM16-AS1	ENST00000662585.1		n.381+5509A>C		intron	N/A
	CEACAM16-AS1	ENST00000702856.2		n.378+5509A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86885 AN: 151770 Hom.: 25095 Cov.: 30

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.573 AC: 86957 AN: 151888 Hom.: 25131 Cov.: 30 AF XY: 0.570 AC XY: 42299 AN XY: 74254

African (AFR) AF: 0.632 AC: 26153 AN: 41406

American (AMR) AF: 0.467 AC: 7128 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3470

East Asian (EAS) AF: 0.587 AC: 3012 AN: 5134

South Asian (SAS) AF: 0.670 AC: 3223 AN: 4814

European-Finnish (FIN) AF: 0.533 AC: 5644 AN: 10584

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.569 AC: 38628 AN: 67912

Other (OTH) AF: 0.535 AC: 1130 AN: 2112

Alfa AF: 0.557 Hom.: 43089

Bravo AF: 0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4802234; hg19: chr19-45222600;