chr1-171683838-T-C

Position:

• chr1-171683838-T-C

Variant summary

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

The ENST00000428881.1(RPL4P3):​n.601A>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 0.193 in 727,340 control chromosomes in the GnomAD database, including 14,279 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 0.20 (3286 hom., cov: 31)
  • Exomes 𝑓: 0.19 (10993 hom.)
• Consequence: RPL4P3 ENST00000428881.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

Genes affected

RPL4P3 (HGNC:35773): (ribosomal protein L4 pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL4P3	ENST00000428881.1	n.601A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30975 AN: 151994 Hom.: 3286 Cov.: 31

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.190 AC: 109496 AN: 575226 Hom.: 10993 Cov.: 6 AF XY: 0.191 AC XY: 59566 AN XY: 311486

Gnomad4 AFR exome AF: 0.256

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.209

Gnomad4 EAS exome AF: 0.107

Gnomad4 SAS exome AF: 0.199

Gnomad4 FIN exome AF: 0.164

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.196

GnomAD4 genome AF: 0.204 AC: 30995 AN: 152114 Hom.: 3286 Cov.: 31 AF XY: 0.202 AC XY: 15010 AN XY: 74368

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.211

Alfa AF: 0.200 Hom.: 3856

Bravo AF: 0.207

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.27
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11799420; hg19: chr1-171652978;