3-33798239-C-CCCTGTGCATTACGTA

Variant names:

• chr3-33798239-C-CCCTGTGCATTACGTA
• rs28381975
• ENST00000747835.1:n.8_9insTACGTAATGCACAGG

Variant summary

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

The ENST00000747835.1(PDCD6IP-DT):​n.8_9insTACGTAATGCACAGG variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 20)
• Consequence: PDCD6IP-DT ENST00000747835.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDCD6IP-DT	NR_183730.1	n.280_281insTACGTAATGCACAGG		non_coding_transcript_exon_variant	Exon 1 of 2
PDCD6IP-DT	NR_183731.1	n.125+155_125+156insTACGTAATGCACAGG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDCD6IP-DT	ENST00000747835.1	n.8_9insTACGTAATGCACAGG		non_coding_transcript_exon_variant	Exon 1 of 4
PDCD6IP-DT	ENST00000747836.1	n.7_8insTACGTAATGCACAGG		non_coding_transcript_exon_variant	Exon 1 of 3
PDCD6IP-DT	ENST00000747840.1	n.790_791insTACGTAATGCACAGG		non_coding_transcript_exon_variant	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

Alfa AF: 0.00 Hom.: 196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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;