ENST00000399492.6:n.656+1093delT

Variant names:

• chr12-6442452-CA-C
• rs35471040
• ENST00000399492.6:n.656+1093delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000399492.6(CD27-AS1):​n.656+1093delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (6439 hom., cov: 0)
• Consequence: CD27-AS1 ENST00000399492.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 1 publications found

Genes affected

CD27-AS1 (HGNC:43896): (CD27 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399492.6. 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
	CD27-AS1	NR_015382.2		n.1688+1093delT		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD27-AS1	ENST00000399492.6	TSL:1	n.656+1093delT		intron	N/A
	CD27-AS1	ENST00000417058.6	TSL:1	n.985+1093delT		intron	N/A
	CD27-AS1	ENST00000537003.2	TSL:1	n.2151+1093delT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.433 AC: 42606 AN: 98508 Hom.: 6442 Cov.: 0

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.514

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.432 AC: 42596 AN: 98498 Hom.: 6439 Cov.: 0 AF XY: 0.433 AC XY: 19941 AN XY: 46014

African (AFR) AF: 0.449 AC: 11316 AN: 25190

American (AMR) AF: 0.453 AC: 4042 AN: 8920

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1248 AN: 2674

East Asian (EAS) AF: 0.407 AC: 1387 AN: 3412

South Asian (SAS) AF: 0.348 AC: 954 AN: 2740

European-Finnish (FIN) AF: 0.454 AC: 1679 AN: 3702

Middle Eastern (MID) AF: 0.516 AC: 99 AN: 192

European-Non Finnish (NFE) AF: 0.422 AC: 20961 AN: 49616

Other (OTH) AF: 0.425 AC: 571 AN: 1344

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs35471040; hg19: chr12-6551618;