3-33798239-C-CCCTGTGCATTCCGTA

Variant names:

• chr3-33798239-C-CCCTGTGCATTCCGTA
• rs28381975
• NR_183730.1:n.280_281insTACGGAATGCACAGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_183730.1(PDCD6IP-DT):​n.280_281insTACGGAATGCACAGG variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,526 control chromosomes in the GnomAD database, including 6,617 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.29 (6602 hom., cov: 20)
  • Exomes 𝑓: 0.15 (15 hom.)
• Consequence: PDCD6IP-DT NR_183730.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDCD6IP-DT	NR_183730.1	n.280_281insTACGGAATGCACAGG		non_coding_transcript_exon_variant	Exon 1 of 2
PDCD6IP-DT	NR_183731.1	n.125+155_125+156insTACGGAATGCACAGG		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDCD6IP-DT	ENST00000604982.2	n.145+155_145+156insTACGGAATGCACAGG		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43918 AN: 151754 Hom.: 6579 Cov.: 20

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.304

GnomAD4 exome AF: 0.150 AC: 98 AN: 654 Hom.: 15 AF XY: 0.166 AC XY: 58 AN XY: 350

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.284

Gnomad4 ASJ exome AF: 0.0625

Gnomad4 EAS exome AF: 0.278

Gnomad4 SAS exome AF: 0.175

Gnomad4 FIN exome AF: 0.0833

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.0789

GnomAD4 genome AF: 0.290 AC: 43987 AN: 151872 Hom.: 6602 Cov.: 20 AF XY: 0.293 AC XY: 21706 AN XY: 74206

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.308

Alfa AF: 0.125 Hom.: 196

Asia WGS AF: 0.365 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28381975; hg19: chr3-33839731;