rs2590504

chr9-135473649-C-T

Variant summary

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

The ENST00000660718.1(PPP1R26-AS1):n.63-1072G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,088 control chromosomes in the GnomAD database, including 30,812 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 0.61 (30812 hom., cov: 32)
• Consequence: PPP1R26-AS1 ENST00000660718.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

PPP1R26-AS1 (HGNC:48717): (PPP1R26 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 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
PPP1R26-AS1	ENST00000660718.1	n.63-1072G>A		intron_variant, non_coding_transcript_variant
PPP1R26-AS1	ENST00000455039.3	n.106-4940G>A		intron_variant, non_coding_transcript_variant		4
PPP1R26-AS1	ENST00000605260.1	n.47-1656G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92786 AN: 151970 Hom.: 30747 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.611 AC: 92910 AN: 152088 Hom.: 30812 Cov.: 32 AF XY: 0.601 AC XY: 44688 AN XY: 74342

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.587

Alfa AF: 0.530 Hom.: 35678

Bravo AF: 0.641

Asia WGS AF: 0.594 AC: 2066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.66
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2590504; hg19: chr9-138365495; COSMIC: COSV72003161;