rs10521746

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chrX-128313889-G-A
• chrX-128313889-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL7AP72		n.128313889G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL7AP72	ENST00000417266.1	n.609G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000225689	ENST00000660383.1	n.1168+9608C>T		intron_variant	Intron 9 of 10

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 v4.3

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;