chr6-28732575-T-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPSAP2		n.28732575T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPSAP2	ENST00000416785.1	n.559T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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;