ENST00000416785.1:n.559T>G

Variant names:

• chr6-28732575-T-G
• rs6456834
• ENST00000416785.1:n.559T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416785.1(RPSAP2):​n.559T>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.845 in 725,688 control chromosomes in the GnomAD database, including 262,985 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 0.77 (47339 hom., cov: 32)
  • Exomes 𝑓: 0.86 (215646 hom.)
• Consequence: RPSAP2 ENST00000416785.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.04
• Publications: 20 publications found

Genes affected

RPSAP2 (HGNC:18771): (ribosomal protein SA pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416785.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPSAP2	ENST00000416785.1	TSL:6	n.559T>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117585 AN: 152056 Hom.: 47330 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.772

GnomAD4 exome AF: 0.863 AC: 495215 AN: 573514 Hom.: 215646 Cov.: 2 AF XY: 0.867 AC XY: 272873 AN XY: 314914

African (AFR) AF: 0.517 AC: 8588 AN: 16600

American (AMR) AF: 0.874 AC: 36533 AN: 41782

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 16137 AN: 19496

East Asian (EAS) AF: 0.984 AC: 32291 AN: 32814

South Asian (SAS) AF: 0.890 AC: 61318 AN: 68926

European-Finnish (FIN) AF: 0.948 AC: 33562 AN: 35416

Middle Eastern (MID) AF: 0.862 AC: 2098 AN: 2434

European-Non Finnish (NFE) AF: 0.857 AC: 279089 AN: 325714

Other (OTH) AF: 0.844 AC: 25599 AN: 30332

GnomAD4 genome AF: 0.773 AC: 117629 AN: 152174 Hom.: 47339 Cov.: 32 AF XY: 0.783 AC XY: 58260 AN XY: 74412

African (AFR) AF: 0.530 AC: 21996 AN: 41466

American (AMR) AF: 0.828 AC: 12672 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2896 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5061 AN: 5186

South Asian (SAS) AF: 0.889 AC: 4290 AN: 4824

European-Finnish (FIN) AF: 0.952 AC: 10105 AN: 10612

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57934 AN: 67994

Other (OTH) AF: 0.775 AC: 1639 AN: 2114

Alfa AF: 0.794 Hom.: 75000

Bravo AF: 0.749

Asia WGS AF: 0.919 AC: 3197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.6
DANN	Benign	0.31
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs6456834; hg19: chr6-28700352;