rs7250339

Variant names:

• chr19-44642312-A-G
• rs7250339
• ENST00000590796.1:n.409-9693T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000590796.1(CEACAM16-AS1):​n.409-9693T>C variant causes a intron 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 ENST00000590796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• Publications: 8 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=-0.92).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEACAM16-AS1	ENST00000590796.1	n.409-9693T>C		intron_variant	Intron 3 of 3	5
CEACAM16-AS1	ENST00000662585.1	n.476-9693T>C		intron_variant	Intron 2 of 2
CEACAM16-AS1	ENST00000810360.1	n.90+1414T>C		intron_variant	Intron 1 of 2
CEACAM16-AS1	ENST00000810361.1	n.62+2230T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.372 AC: 15406 AN: 41400

American (AMR) AF: 0.250 AC: 3812 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3460

East Asian (EAS) AF: 0.457 AC: 2357 AN: 5162

South Asian (SAS) AF: 0.390 AC: 1879 AN: 4812

European-Finnish (FIN) AF: 0.217 AC: 2297 AN: 10586

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.245 AC: 16636 AN: 67960

Other (OTH) AF: 0.277 AC: 584 AN: 2112

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs7250339; hg19: chr19-45145612;