rs11008032

Positions:

• chr10-30403458-C-G

Variant summary

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

The ENST00000438347.1(CCND3P1):​n.319G>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0769 in 350,452 control chromosomes in the GnomAD database, including 1,231 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 0.077 (559 hom., cov: 32)
  • Exomes 𝑓: 0.077 (672 hom.)
• Consequence: CCND3P1 ENST00000438347.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.70

Genes affected

CCND3P1 (HGNC:1586): (cyclin D3 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 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
CCND3P1	ENST00000438347.1	n.319G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11667 AN: 152160 Hom.: 557 Cov.: 32

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0813

Gnomad OTH AF: 0.0955

GnomAD4 exome AF: 0.0770 AC: 15255 AN: 198174 Hom.: 672 Cov.: 0 AF XY: 0.0766 AC XY: 8680 AN XY: 113352

Gnomad4 AFR exome AF: 0.0279

Gnomad4 AMR exome AF: 0.121

Gnomad4 ASJ exome AF: 0.120

Gnomad4 EAS exome AF: 0.163

Gnomad4 SAS exome AF: 0.0725

Gnomad4 FIN exome AF: 0.0714

Gnomad4 NFE exome AF: 0.0679

Gnomad4 OTH exome AF: 0.0766

GnomAD4 genome AF: 0.0767 AC: 11683 AN: 152278 Hom.: 559 Cov.: 32 AF XY: 0.0790 AC XY: 5883 AN XY: 74450

Gnomad4 AFR AF: 0.0334

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.0905

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.0813

Gnomad4 OTH AF: 0.0997

Alfa AF: 0.0681 Hom.: 54

Bravo AF: 0.0790

Asia WGS AF: 0.182 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	0.61
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11008032; hg19: chr10-30692387;