rs11008032

Variant names:

• chr10-30403458-C-G
• rs11008032
• ENST00000438347.1:n.319G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438347.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCND3P1	ENST00000438347.1	TSL:6	n.319G>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.0279 AC: 111 AN: 3980

American (AMR) AF: 0.121 AC: 1657 AN: 13746

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 441 AN: 3684

East Asian (EAS) AF: 0.163 AC: 1129 AN: 6912

South Asian (SAS) AF: 0.0725 AC: 2663 AN: 36728

European-Finnish (FIN) AF: 0.0714 AC: 1540 AN: 21564

Middle Eastern (MID) AF: 0.119 AC: 145 AN: 1222

European-Non Finnish (NFE) AF: 0.0679 AC: 6886 AN: 101426

Other (OTH) AF: 0.0766 AC: 683 AN: 8912

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

African (AFR) AF: 0.0334 AC: 1387 AN: 41570

American (AMR) AF: 0.116 AC: 1781 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3468

East Asian (EAS) AF: 0.176 AC: 912 AN: 5188

South Asian (SAS) AF: 0.0905 AC: 437 AN: 4828

European-Finnish (FIN) AF: 0.0848 AC: 899 AN: 10600

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0813 AC: 5530 AN: 68014

Other (OTH) AF: 0.0997 AC: 211 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	0.61
DANN	Benign	0.28
PhyloP100		3.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11008032;

hg19: chr10-30692387;