X-128313889-G-A

Position:

• chrX-128313889-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL7AP72	ENST00000417266.1	n.609G>A		non_coding_transcript_exon_variant	1/1
	ENST00000660383.1	n.1168+9608C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 8789 AN: 111325 Hom.: 362 Cov.: 23 AF XY: 0.0808 AC XY: 2710 AN XY: 33527

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

Gnomad4 FIN exome AF: 0.0556

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.0365

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.0895

Gnomad4 EAS AF: 0.0290

Gnomad4 SAS AF: 0.0642

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.0788

Gnomad4 OTH AF: 0.0934

Alfa AF: 0.0467 Hom.: 323

Bravo AF: 0.0912

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521746; hg19: chrX-127447867;