chr10-91544895-T-A

Variant names:

• chr10-91544895-T-A
• rs1928494
• ENST00000450552.1:n.44T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

HECTD2-AS1 (HGNC:):

HECTD2-AS1 (HGNC:48679): (HECTD2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450552.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HECTD2-AS1	NR_024467.1		n.111-5317A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPS27P1	ENST00000450552.1	TSL:6	n.44T>A		non_coding_transcript_exon	Exon 1 of 1
	HECTD2-AS1	ENST00000688440.2		n.247-19746A>T		intron	N/A
	HECTD2-AS1	ENST00000700888.2		n.97-19746A>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.844 AC: 27 AN: 32

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.987 AC: 41059 AN: 41580

American (AMR) AF: 0.971 AC: 14858 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3455 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5186 AN: 5188

South Asian (SAS) AF: 0.991 AC: 4786 AN: 4828

European-Finnish (FIN) AF: 0.937 AC: 9944 AN: 10614

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63242 AN: 68032

Other (OTH) AF: 0.970 AC: 2051 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs1928494; hg19: chr10-93304652;