chrX-128313889-G-A

Variant names:

• chrX-128313889-G-A
• rs10521746
• ENST00000417266.1:n.609G>A

Variant summary

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

The ENST00000417266.1(RPL7AP72):​n.609G>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 0.0792 in 111,451 control chromosomes in the GnomAD database, including 368 homozygotes. There are 2,728 hemizygotes in GnomAD. 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 0.079 (368 hom., 2726 hem., cov: 23)
  • Exomes 𝑓: 0.065 (0 hom. 2 hem.)
• Consequence: RPL7AP72 ENST00000417266.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 0 publications found

Genes affected

RPL7AP72 (HGNC:36442): (ribosomal protein L7a pseudogene 72)

ENSG00000225689 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417266.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL7AP72	ENST00000417266.1	TSL:6	n.609G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000225689	ENST00000660383.1		n.1168+9608C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 8789 AN: 111325 Hom.: 362 Cov.: 23

Gnomad AFR AF: 0.0365

Gnomad AMI AF: 0.0660

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.0895

Gnomad EAS AF: 0.0286

Gnomad SAS AF: 0.0618

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.0335

Gnomad NFE AF: 0.0787

Gnomad OTH AF: 0.0945

GnomAD4 exome AF: 0.0649 AC: 5 AN: 77 Hom.: 0 Cov.: 0 AF XY: 0.0645 AC XY: 2 AN XY: 31

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: 0.0556 AC: 3 AN: 54

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 2 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 3

GnomAD4 genome AF: 0.0792 AC: 8819 AN: 111374 Hom.: 368 Cov.: 23 AF XY: 0.0812 AC XY: 2726 AN XY: 33586

African (AFR) AF: 0.0365 AC: 1120 AN: 30716

American (AMR) AF: 0.217 AC: 2253 AN: 10384

Ashkenazi Jewish (ASJ) AF: 0.0895 AC: 237 AN: 2649

East Asian (EAS) AF: 0.0290 AC: 102 AN: 3521

South Asian (SAS) AF: 0.0642 AC: 171 AN: 2662

European-Finnish (FIN) AF: 0.0939 AC: 564 AN: 6004

Middle Eastern (MID) AF: 0.0413 AC: 9 AN: 218

European-Non Finnish (NFE) AF: 0.0788 AC: 4177 AN: 53028

Other (OTH) AF: 0.0934 AC: 141 AN: 1510

Alfa AF: 0.0467 Hom.: 323

Bravo AF: 0.0912

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.78
DANN	Benign	0.52
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10521746; hg19: chrX-127447867;