1-99231507-G-T

Variant names:

• chr1-99231507-G-T
• rs819750
• ENST00000647692.1:n.524-11310G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647692.1(PLPPR5-AS1):​n.524-11310G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.922 in 152,096 control chromosomes in the GnomAD database, including 64,844 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 0.92 (64844 hom., cov: 31)
• Consequence: PLPPR5-AS1 ENST00000647692.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

PLPPR5-AS1 (HGNC:55720): (PLPPR5 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPPR5-AS1	ENST00000647692.1	n.524-11310G>T		intron_variant	Intron 4 of 4
PLPPR5-AS1	ENST00000658279.1	n.412-11310G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140150 AN: 151978 Hom.: 64780 Cov.: 31

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.919

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.922 AC: 140273 AN: 152096 Hom.: 64844 Cov.: 31 AF XY: 0.925 AC XY: 68728 AN XY: 74332

Gnomad4 AFR AF: 0.976

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.920

Alfa AF: 0.891 Hom.: 23339

Bravo AF: 0.926

Asia WGS AF: 0.969 AC: 3369 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.44
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs819750; hg19: chr1-99697063;