12-6442452-C-CAA

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000399492.6(CD27-AS1):​n.656+1093_656+1094insTT 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 0.000010 (0 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: Uncertain_significance. The variant received 0 ACMG points.

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+1092_1688+1093dupTT		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+1094insTT		intron	N/A
	CD27-AS1	ENST00000417058.6	TSL:1	n.985+1093_985+1094insTT		intron	N/A
	CD27-AS1	ENST00000537003.2	TSL:1	n.2151+1093_2151+1094insTT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000102 AC: 1 AN: 98426 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000202

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000102 AC: 1 AN: 98426 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 45938

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 25120

American (AMR) AF: 0.00 AC: 0 AN: 8900

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2682

East Asian (EAS) AF: 0.00 AC: 0 AN: 3430

South Asian (SAS) AF: 0.00 AC: 0 AN: 2754

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3706

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 210

European-Non Finnish (NFE) AF: 0.0000202 AC: 1 AN: 49578

Other (OTH) AF: 0.00 AC: 0 AN: 1334

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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;