3-33798239-C-CCCTGTGCATT

Variant names:

• chr3-33798239-C-CCCTGTGCATT
• rs28381975
• ENST00000747835.1:n.8_9insAATGCACAGG

Variant summary

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

The NR_183730.1(PDCD6IP-DT):​n.280_281insAATGCACAGG variant causes a non coding transcript exon 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: not found (cov: 20)
• Consequence: PDCD6IP-DT NR_183730.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 0 publications found

Genes affected

PDCD6IP-DT (HGNC:55244): (PDCD6IP divergent transcript)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183730.1. 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
	PDCD6IP-DT	NR_183730.1		n.280_281insAATGCACAGG		non_coding_transcript_exon	Exon 1 of 2
	PDCD6IP-DT	NR_183731.1		n.125+155_125+156insAATGCACAGG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDCD6IP-DT	ENST00000747835.1		n.8_9insAATGCACAGG		non_coding_transcript_exon	Exon 1 of 4
	PDCD6IP-DT	ENST00000747836.1		n.7_8insAATGCACAGG		non_coding_transcript_exon	Exon 1 of 3
	PDCD6IP-DT	ENST00000747840.1		n.790_791insAATGCACAGG		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 20

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

GnomAD4 genome Cov.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs28381975; hg19: chr3-33839731;