19-7665708-G-A

Variant names:

• chr19-7665708-G-A
• rs12460483
• XR_007067117.1:n.30G>A

Variant summary

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

The XR_007067117.1(RPS27AP19):​n.30G>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 0.0663 in 279,458 control chromosomes in the GnomAD database, including 937 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 0.089 (803 hom., cov: 32)
  • Exomes 𝑓: 0.039 (134 hom.)
• Consequence: RPS27AP19 XR_007067117.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 1 publications found

Genes affected

RPS27AP19 (HGNC:52298): (RPS27A pseudogene 19)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPS27AP19	XR_007067117.1	n.30G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPS27AP19	ENST00000597285.1	n.-9G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0892 AC: 13556 AN: 152006 Hom.: 800 Cov.: 32

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0944

GnomAD4 exome AF: 0.0391 AC: 4973 AN: 127334 Hom.: 134 Cov.: 0 AF XY: 0.0391 AC XY: 3000 AN XY: 76694

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00491 AC: 16 AN: 3260

American (AMR) AF: 0.0602 AC: 454 AN: 7542

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 168 AN: 3914

East Asian (EAS) AF: 0.00528 AC: 26 AN: 4920

South Asian (SAS) AF: 0.0459 AC: 1180 AN: 25720

European-Finnish (FIN) AF: 0.0501 AC: 275 AN: 5494

Middle Eastern (MID) AF: 0.0273 AC: 12 AN: 440

European-Non Finnish (NFE) AF: 0.0376 AC: 2636 AN: 70062

Other (OTH) AF: 0.0344 AC: 206 AN: 5982

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0891 AC: 13561 AN: 152124 Hom.: 803 Cov.: 32 AF XY: 0.0896 AC XY: 6660 AN XY: 74370

African (AFR) AF: 0.0217 AC: 900 AN: 41522

American (AMR) AF: 0.144 AC: 2192 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3472

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5180

South Asian (SAS) AF: 0.113 AC: 544 AN: 4816

European-Finnish (FIN) AF: 0.125 AC: 1318 AN: 10584

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7798 AN: 67984

Other (OTH) AF: 0.0930 AC: 196 AN: 2108

Alfa AF: 0.0791 Hom.: 247

Bravo AF: 0.0895

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.67
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs12460483; hg19: chr19-7730594;