rs2271751

chr10-103415374-T-C

Variant summary

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

The NM_014976.2(PDCD11):c.1518+223T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,158 control chromosomes in the GnomAD database, including 6,682 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 0.27 (6682 hom., cov: 32)
• Consequence: PDCD11 NM_014976.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDCD11	NM_014976.2	c.1518+223T>C		intron_variant		ENST00000369797.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDCD11	ENST00000369797.8	c.1518+223T>C		intron_variant		1	NM_014976.2	P4
PDCD11	ENST00000649849.1	c.1518+223T>C		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41288 AN: 152040 Hom.: 6678 Cov.: 32

Gnomad AFR AF: 0.0929

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.282

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.271 AC: 41293 AN: 152158 Hom.: 6682 Cov.: 32 AF XY: 0.278 AC XY: 20696 AN XY: 74374

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.282

Alfa AF: 0.283 Hom.: 1703

Bravo AF: 0.252

Asia WGS AF: 0.400 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.33
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: rs2271751; hg19: chr10-105175131;