rs7255066

chr19-44642803-T-C

Variant summary

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

The ENST00000662585.1(CEACAM16-AS1):n.476-10184A>G variant causes a intron, non coding transcript 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 ENST00000662585.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEACAM16-AS1	ENST00000662585.1	n.476-10184A>G		intron_variant, non_coding_transcript_variant
CEACAM16-AS1	ENST00000590796.1	n.409-10184A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.380

Alfa AF: 0.287 Hom.: 14806

Bravo AF: 0.442

Asia WGS AF: 0.457 AC: 1590 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	0.014
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7255066; hg19: chr19-45146103;