chr21-44999280-G-A

Variant names:

• chr21-44999280-G-A
• rs8134028
• ENST00000615826.2:n.687C>T

Variant summary

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

The ENST00000615826.2(PICSAR):​n.687C>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 ENST00000615826.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000615826.2	n.687C>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
PICSAR	ENST00000758108.1	n.625C>T		non_coding_transcript_exon_variant	Exon 2 of 2
PICSAR	ENST00000758109.1	n.1094C>T		non_coding_transcript_exon_variant	Exon 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 18

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.332 AC: 13789 AN: 41508

American (AMR) AF: 0.0726 AC: 1111 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.0654 AC: 339 AN: 5180

South Asian (SAS) AF: 0.0899 AC: 434 AN: 4826

European-Finnish (FIN) AF: 0.0263 AC: 279 AN: 10628

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0489 AC: 3328 AN: 68028

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.0450 Hom.: 87

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs8134028; hg19: chr21-46419194;