9-14041072-T-C

Variant names:

• chr9-14041072-T-C
• rs10511588
• ENST00000434028.1:n.790A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434028.1(RPL3P11):​n.790A>G 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 0.558 in 316,836 control chromosomes in the GnomAD database, including 51,050 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 0.56 (24192 hom., cov: 33)
  • Exomes 𝑓: 0.56 (26858 hom.)
• Consequence: RPL3P11 ENST00000434028.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.03
• Publications: 2 publications found

Genes affected

RPL3P11 (HGNC:35521): (ribosomal protein L3 pseudogene 11)

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 = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL3P11		n.14041072T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL3P11	ENST00000434028.1	n.790A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84527 AN: 152012 Hom.: 24153 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.491

GnomAD4 exome AF: 0.559 AC: 92133 AN: 164708 Hom.: 26858 Cov.: 0 AF XY: 0.564 AC XY: 52020 AN XY: 92300

African (AFR) AF: 0.593 AC: 2408 AN: 4062

American (AMR) AF: 0.455 AC: 5665 AN: 12460

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1479 AN: 3346

East Asian (EAS) AF: 0.953 AC: 6587 AN: 6914

South Asian (SAS) AF: 0.625 AC: 17407 AN: 27838

European-Finnish (FIN) AF: 0.601 AC: 5342 AN: 8890

Middle Eastern (MID) AF: 0.455 AC: 225 AN: 494

European-Non Finnish (NFE) AF: 0.524 AC: 48509 AN: 92520

Other (OTH) AF: 0.551 AC: 4511 AN: 8184

GnomAD4 genome AF: 0.556 AC: 84625 AN: 152128 Hom.: 24192 Cov.: 33 AF XY: 0.562 AC XY: 41789 AN XY: 74350

African (AFR) AF: 0.588 AC: 24398 AN: 41522

American (AMR) AF: 0.478 AC: 7305 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3470

East Asian (EAS) AF: 0.953 AC: 4934 AN: 5180

South Asian (SAS) AF: 0.646 AC: 3108 AN: 4808

European-Finnish (FIN) AF: 0.596 AC: 6311 AN: 10584

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35441 AN: 67966

Other (OTH) AF: 0.497 AC: 1049 AN: 2110

Alfa AF: 0.468 Hom.: 3449

Bravo AF: 0.546

Asia WGS AF: 0.787 AC: 2732 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	11
DANN	Benign	0.33
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs10511588; hg19: chr9-14041071;