rs2590504

Variant names:

• chr9-135473649-C-T
• rs2590504
• ENST00000455039.3:n.106-4940G>A

Variant summary

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

The ENST00000455039.3(PPP1R26-AS1):​n.106-4940G>A variant causes a intron 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 ENST00000455039.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444
• Publications: 8 publications found

Genes affected

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

ENSG00000299651 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455039.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R26-AS1	ENST00000455039.3	TSL:4	n.106-4940G>A		intron	N/A
	PPP1R26-AS1	ENST00000605260.1	TSL:4	n.47-1656G>A		intron	N/A
	PPP1R26-AS1	ENST00000660718.1		n.63-1072G>A		intron	N/A

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

African (AFR) AF: 0.883 AC: 36657 AN: 41518

American (AMR) AF: 0.572 AC: 8738 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1656 AN: 3470

East Asian (EAS) AF: 0.616 AC: 3177 AN: 5154

South Asian (SAS) AF: 0.464 AC: 2226 AN: 4802

European-Finnish (FIN) AF: 0.368 AC: 3897 AN: 10588

Middle Eastern (MID) AF: 0.472 AC: 137 AN: 290

European-Non Finnish (NFE) AF: 0.513 AC: 34866 AN: 67970

Other (OTH) AF: 0.587 AC: 1240 AN: 2112

Alfa AF: 0.546 Hom.: 93425

Bravo AF: 0.641

Asia WGS AF: 0.594 AC: 2066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.57
PhyloP100		-0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2590504;

hg19: chr9-138365495;

COSMIC: COSV72003161;