rs7277744

chr21-45004654-C-T

Variant summary

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

The NR_024089.2(PICSAR):n.74G>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 152,040 control chromosomes in the GnomAD database, including 16,078 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 (16073 hom., cov: 31)
  • Exomes 𝑓: 0.55 (5 hom.)
• Consequence: PICSAR NR_024089.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989

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=-0.94).
• 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.74G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PICSAR	ENST00000615826.1	n.74G>A		non_coding_transcript_exon_variant	1/2	1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65522 AN: 151884 Hom.: 16060 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.474

GnomAD4 exome AF: 0.553 AC: 21 AN: 38 Hom.: 5 Cov.: 0 AF XY: 0.625 AC XY: 20 AN XY: 32

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.550

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.431 AC: 65562 AN: 152002 Hom.: 16073 Cov.: 31 AF XY: 0.441 AC XY: 32782 AN XY: 74288

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.474

Alfa AF: 0.460 Hom.: 2897

Bravo AF: 0.428

Asia WGS AF: 0.644 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.4
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7277744; hg19: chr21-46424569;