3-33798239-C-CCCTGTGCATTCCGTA

Variant names:

• chr3-33798239-C-CCCTGTGCATTCCGTA
• rs28381975
• ENST00000747835.1:n.8_9insTACGGAATGCACAGG

Variant summary

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

The ENST00000747835.1(PDCD6IP-DT):​n.8_9insTACGGAATGCACAGG 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. 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: 𝑓 0.29 (6602 hom., cov: 20)
  • Exomes 𝑓: 0.15 (15 hom.)
• 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: Benign. The variant received -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	ENST00000747835.1	n.8_9insTACGGAATGCACAGG		non_coding_transcript_exon_variant	Exon 1 of 4
PDCD6IP-DT	ENST00000747836.1	n.7_8insTACGGAATGCACAGG		non_coding_transcript_exon_variant	Exon 1 of 3
PDCD6IP-DT	ENST00000747840.1	n.790_791insTACGGAATGCACAGG		non_coding_transcript_exon_variant	Exon 1 of 2

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

African (AFR) AF: 0.167 AC: 2 AN: 12

American (AMR) AF: 0.284 AC: 29 AN: 102

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 1 AN: 16

East Asian (EAS) AF: 0.278 AC: 5 AN: 18

South Asian (SAS) AF: 0.175 AC: 7 AN: 40

European-Finnish (FIN) AF: 0.0833 AC: 1 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.120 AC: 50 AN: 416

Other (OTH) AF: 0.0789 AC: 3 AN: 38

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

African (AFR) AF: 0.292 AC: 12072 AN: 41400

American (AMR) AF: 0.391 AC: 5965 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1009 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2087 AN: 5130

South Asian (SAS) AF: 0.333 AC: 1604 AN: 4812

European-Finnish (FIN) AF: 0.241 AC: 2539 AN: 10552

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17803 AN: 67924

Other (OTH) AF: 0.308 AC: 651 AN: 2112

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

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;