rs1928494

chr10-91544895-T-Achr10-91544895-T-Cchr10-91544895-T-G

Variant summary

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

The ENST00000450552.1(RPS27P1):n.44T>A 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 0.957 in 152,376 control chromosomes in the GnomAD database, including 69,831 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 0.96 (69818 hom., cov: 33)
  • Exomes 𝑓: 0.86 (13 hom.)
• Consequence: RPS27P1 ENST00000450552.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

RPS27P1 (HGNC:23740): (ribosomal protein S27 pseudogene 1)

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HECTD2-AS1	NR_024467.1	n.111-5317A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS27P1	ENST00000450552.1	n.44T>A		non_coding_transcript_exon_variant	1/1
	ENST00000688440.1	n.200-19746A>T		intron_variant, non_coding_transcript_variant
	ENST00000700888.1	n.97-19746A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145657 AN: 152222 Hom.: 69760 Cov.: 33

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.970

GnomAD4 exome AF: 0.861 AC: 31 AN: 36 Hom.: 13 Cov.: 0 AF XY: 0.917 AC XY: 22 AN XY: 24

Gnomad4 FIN exome AF: 0.844

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.957 AC: 145774 AN: 152340 Hom.: 69818 Cov.: 33 AF XY: 0.959 AC XY: 71416 AN XY: 74484

Gnomad4 AFR AF: 0.987

Gnomad4 AMR AF: 0.971

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.991

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.970

Alfa AF: 0.944 Hom.: 8425

Bravo AF: 0.961

Asia WGS AF: 0.992 AC: 3452 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	1.3
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1928494; hg19: chr10-93304652;