ENST00000399492.6:n.656+1092_656+1093delTT

Variant names:

• chr12-6442452-CAA-C
• rs35471040
• ENST00000399492.6:n.656+1092_656+1093delTT

Variant summary

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

The ENST00000399492.6(CD27-AS1):​n.656+1092_656+1093delTT 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 0.16 (813 hom., cov: 0)
• Consequence: CD27-AS1 ENST00000399492.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• 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 (NFE) allele frequency at 95% confidence interval = 0.171 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD27-AS1	NR_015382.2		n.1688+1092_1688+1093delTT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD27-AS1	ENST00000399492.6	TSL:1	n.656+1092_656+1093delTT		intron	N/A
	CD27-AS1	ENST00000417058.6	TSL:1	n.985+1092_985+1093delTT		intron	N/A
	CD27-AS1	ENST00000537003.2	TSL:1	n.2151+1092_2151+1093delTT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 15685 AN: 98470 Hom.: 811 Cov.: 0

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.159 AC: 15688 AN: 98454 Hom.: 813 Cov.: 0 AF XY: 0.157 AC XY: 7205 AN XY: 45972

African (AFR) AF: 0.133 AC: 3342 AN: 25178

American (AMR) AF: 0.153 AC: 1369 AN: 8920

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 485 AN: 2682

East Asian (EAS) AF: 0.134 AC: 457 AN: 3420

South Asian (SAS) AF: 0.112 AC: 306 AN: 2734

European-Finnish (FIN) AF: 0.199 AC: 740 AN: 3712

Middle Eastern (MID) AF: 0.158 AC: 30 AN: 190

European-Non Finnish (NFE) AF: 0.174 AC: 8608 AN: 49560

Other (OTH) AF: 0.156 AC: 210 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		1.3

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;