ENST00000615826.1:n.661C>T

Variant names:

• chr21-44999280-G-A
• rs8134028
• ENST00000615826.1:n.661C>T

Variant summary

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

The ENST00000615826.1(PICSAR):​n.661C>T 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 0.13 in 152,270 control chromosomes in the GnomAD database, including 2,518 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 0.13 (2518 hom., cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PICSAR ENST00000615826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PICSAR	NR_024089.2	n.661C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PICSAR	ENST00000615826.1	n.661C>T		non_coding_transcript_exon_variant	Exon 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19703 AN: 152152 Hom.: 2505 Cov.: 34

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0489

Gnomad OTH AF: 0.126

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 16

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.130 AC: 19754 AN: 152270 Hom.: 2518 Cov.: 34 AF XY: 0.125 AC XY: 9321 AN XY: 74464

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.0726

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0654

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0489

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0323 Hom.: 53

Bravo AF: 0.142

Asia WGS AF: 0.113 AC: 393 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
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: rs8134028; hg19: chr21-46419194;