rs889695

chr16-29863614-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000565014.5(CDIPTOSP):n.22T>C 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 0.322 in 152,208 control chromosomes in the GnomAD database, including 8,670 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.32 (8662 hom., cov: 31)
  • Exomes 𝑓: 0.28 (8 hom.)
• Consequence: CDIPTOSP ENST00000565014.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

CDIPTOSP (HGNC:48609): (CDIP transferase opposite strand, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDIPTOSP	ENST00000565014.5	n.22T>C		non_coding_transcript_exon_variant	1/6	2
CDIPTOSP	ENST00000702587.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48844 AN: 151794 Hom.: 8632 Cov.: 31

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.268

GnomAD4 exome AF: 0.277 AC: 82 AN: 296 Hom.: 8 Cov.: 0 AF XY: 0.275 AC XY: 61 AN XY: 222

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 0.290

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.256

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.322 AC: 48916 AN: 151912 Hom.: 8662 Cov.: 31 AF XY: 0.317 AC XY: 23527 AN XY: 74236

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.265

Alfa AF: 0.327 Hom.: 1343

Bravo AF: 0.319

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.2
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs889695; hg19: chr16-29874935;