rs13047060

Positions:

• chr21-45004592-G-T
• chr21-45004592-G-C
• chr21-45004592-G-A

Variant summary

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

The NR_024089.2(PICSAR):​n.136C>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 0.431 in 152,148 control chromosomes in the GnomAD database, including 16,541 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 0.43 (16522 hom., cov: 32)
  • Exomes 𝑓: 0.44 (19 hom.)
• Consequence: PICSAR NR_024089.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

PICSAR (HGNC:19725): (P38 inhibited cutaneous squamous cell carcinoma associated lincRNA)

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 = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PICSAR	NR_024089.2	n.136C>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PICSAR	ENST00000615826.1	n.136C>A		non_coding_transcript_exon_variant	1/2	1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65522 AN: 151898 Hom.: 16515 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.478

GnomAD4 exome AF: 0.439 AC: 58 AN: 132 Hom.: 19 Cov.: 0 AF XY: 0.404 AC XY: 38 AN XY: 94

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.384

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.431 AC: 65554 AN: 152016 Hom.: 16522 Cov.: 32 AF XY: 0.441 AC XY: 32756 AN XY: 74286

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.477

Alfa AF: 0.324 Hom.: 941

Bravo AF: 0.427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13047060; hg19: chr21-46424507;