rs7250339

Positions:

• chr19-44642312-A-G
• chr19-44642312-A-T

Variant summary

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

The ENST00000662585.1(CEACAM16-AS1):​n.476-9693T>C 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 0.29 in 151,970 control chromosomes in the GnomAD database, including 6,730 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 0.29 (6730 hom., cov: 31)
• Consequence: CEACAM16-AS1 ENST00000662585.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 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.476-9693T>C		intron_variant, non_coding_transcript_variant
CEACAM16-AS1	ENST00000590796.1	n.409-9693T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44049 AN: 151852 Hom.: 6717 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.290 AC: 44103 AN: 151970 Hom.: 6730 Cov.: 31 AF XY: 0.291 AC XY: 21579 AN XY: 74274

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.277

Alfa AF: 0.276 Hom.: 950

Bravo AF: 0.292

Asia WGS AF: 0.414 AC: 1441 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	2.5
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7250339; hg19: chr19-45145612;