19-7665708-G-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XR_007067117.1(RPS27AP19):​n.30G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPS27AP19	XR_007067117.1	n.30G>C		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>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 128442 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 77384

African (AFR) AF: 0.00 AC: 0 AN: 3264

American (AMR) AF: 0.00 AC: 0 AN: 7652

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3970

East Asian (EAS) AF: 0.00 AC: 0 AN: 4924

South Asian (SAS) AF: 0.00 AC: 0 AN: 25978

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5542

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 442

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 70650

Other (OTH) AF: 0.00 AC: 0 AN: 6020

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 247

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.58
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;