rs6480837

Positions:

• chr10-52389483-A-C
• chr10-52389483-A-G
• chr10-52389483-A-T

Variant summary

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

The ENST00000447680.1(RPL31P44):​n.6T>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 0.676 in 475,018 control chromosomes in the GnomAD database, including 111,494 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 0.72 (40340 hom., cov: 30)
  • Exomes 𝑓: 0.66 (71154 hom.)
• Consequence: RPL31P44 ENST00000447680.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

RPL31P44 (HGNC:35523): (ribosomal protein L31 pseudogene 44)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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
RPL31P44	ENST00000447680.1	n.6T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108538 AN: 151760 Hom.: 40268 Cov.: 30

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.663

GnomAD4 exome AF: 0.657 AC: 212459 AN: 323140 Hom.: 71154 Cov.: 0 AF XY: 0.654 AC XY: 118931 AN XY: 181788

Gnomad4 AFR exome AF: 0.913

Gnomad4 AMR exome AF: 0.625

Gnomad4 ASJ exome AF: 0.560

Gnomad4 EAS exome AF: 0.928

Gnomad4 SAS exome AF: 0.644

Gnomad4 FIN exome AF: 0.618

Gnomad4 NFE exome AF: 0.639

Gnomad4 OTH exome AF: 0.666

GnomAD4 genome AF: 0.715 AC: 108668 AN: 151878 Hom.: 40340 Cov.: 30 AF XY: 0.713 AC XY: 52881 AN XY: 74186

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.667

Alfa AF: 0.594 Hom.: 1924

Bravo AF: 0.725

Asia WGS AF: 0.838 AC: 2910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6480837; hg19: chr10-54149243;