ENST00000399492.6:n.656+1093_656+1094insT

Variant names:

• chr12-6442452-C-CA
• rs35471040
• ENST00000399492.6:n.656+1093_656+1094insT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000399492.6(CD27-AS1):​n.656+1093_656+1094insT 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 0.0042 (6 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.

• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00423 (416/98282) while in subpopulation EAS AF = 0.0427 (146/3416). AF 95% confidence interval is 0.0371. There are 6 homozygotes in GnomAd4. There are 200 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD27-AS1	NR_015382.2		n.1688+1093dupT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD27-AS1	ENST00000399492.6	TSL:1	n.656+1093_656+1094insT		intron	N/A
	CD27-AS1	ENST00000417058.6	TSL:1	n.985+1093_985+1094insT		intron	N/A
	CD27-AS1	ENST00000537003.2	TSL:1	n.2151+1093_2151+1094insT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00422 AC: 415 AN: 98294 Hom.: 6 Cov.: 0

Gnomad AFR AF: 0.00315

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00101

Gnomad ASJ AF: 0.00373

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.000540

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00206

Gnomad OTH AF: 0.00375

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

GnomAD4 genome AF: 0.00423 AC: 416 AN: 98282 Hom.: 6 Cov.: 0 AF XY: 0.00436 AC XY: 200 AN XY: 45910

African (AFR) AF: 0.00315 AC: 79 AN: 25116

American (AMR) AF: 0.00101 AC: 9 AN: 8906

Ashkenazi Jewish (ASJ) AF: 0.00373 AC: 10 AN: 2678

East Asian (EAS) AF: 0.0427 AC: 146 AN: 3416

South Asian (SAS) AF: 0.0231 AC: 63 AN: 2730

European-Finnish (FIN) AF: 0.000540 AC: 2 AN: 3706

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 192

European-Non Finnish (NFE) AF: 0.00206 AC: 102 AN: 49484

Other (OTH) AF: 0.00373 AC: 5 AN: 1342

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs35471040; hg19: chr12-6551618;