rs7894407

Variant names:

• chr10-103416422-T-C
• rs7894407
• NM_014976.2:c.1519-69T>C

Variant summary

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

The NM_014976.2(PDCD11):​c.1519-69T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,554,042 control chromosomes in the GnomAD database, including 96,533 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 0.31 (7541 hom., cov: 32)
  • Exomes 𝑓: 0.35 (88992 hom.)
• Consequence: PDCD11 NM_014976.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

PDCD11 (HGNC:13408): (programmed cell death 11) PDCD11 is a NF-kappa-B (NFKB1; 164011)-binding protein that colocalizes with U3 RNA (MIM 180710) in the nucleolus and is required for rRNA maturation and generation of 18S rRNA (Sweet et al., 2003 [PubMed 14624448]; Sweet et al., 2008 [PubMed 17654514]).[supplied by OMIM, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDCD11	NM_014976.2	c.1519-69T>C		intron_variant	Intron 12 of 35	ENST00000369797.8	NP_055791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDCD11	ENST00000369797.8	c.1519-69T>C		intron_variant	Intron 12 of 35	1	NM_014976.2	ENSP00000358812.3
PDCD11	ENST00000649849.1	c.1519-69T>C		intron_variant	Intron 12 of 35			ENSP00000498205.1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46857 AN: 151856 Hom.: 7530 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.322

GnomAD4 exome AF: 0.353 AC: 494948 AN: 1402068 Hom.: 88992 AF XY: 0.350 AC XY: 242861 AN XY: 693560

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.447

Gnomad4 ASJ exome AF: 0.347

Gnomad4 EAS exome AF: 0.457

Gnomad4 SAS exome AF: 0.287

Gnomad4 FIN exome AF: 0.326

Gnomad4 NFE exome AF: 0.357

Gnomad4 OTH exome AF: 0.344

GnomAD4 genome AF: 0.309 AC: 46897 AN: 151974 Hom.: 7541 Cov.: 32 AF XY: 0.309 AC XY: 22960 AN XY: 74296

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.322

Alfa AF: 0.327 Hom.: 1980

Bravo AF: 0.313

Asia WGS AF: 0.370 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.33

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: rs7894407; hg19: chr10-105176179; COSMIC: COSV63933063;