rs7173943

Variant names:

• chr15-99552246-G-C
• rs7173943
• ENST00000471472.2:n.-129C>G

Variant summary

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

The ENST00000471472.2(RPL7P5):​n.-129C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,150 control chromosomes in the GnomAD database, including 33,601 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 0.65 (33585 hom., cov: 30)
  • Exomes 𝑓: 0.37 (16 hom.)
• Consequence: RPL7P5 ENST00000471472.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

Genes affected

RPL7P5 (HGNC:28886): (ribosomal protein L7 pseudogene 5)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL7P5	ENST00000471472.2	n.-129C>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98436 AN: 151774 Hom.: 33537 Cov.: 30

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.372 AC: 96 AN: 258 Hom.: 16 AF XY: 0.372 AC XY: 61 AN XY: 164

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.417

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.365

Gnomad4 OTH exome AF: 0.389

GnomAD4 genome AF: 0.649 AC: 98538 AN: 151892 Hom.: 33585 Cov.: 30 AF XY: 0.649 AC XY: 48122 AN XY: 74184

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.640

Alfa AF: 0.594 Hom.: 3517

Bravo AF: 0.657

Asia WGS AF: 0.655 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7173943; hg19: chr15-100092451;