21-44999277-G-A

Variant names:

• chr21-44999277-G-A
• rs1557362
• ENST00000615826.2:n.690C>T

Variant summary

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

The ENST00000615826.2(PICSAR):​n.690C>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 0.377 in 152,176 control chromosomes in the GnomAD database, including 14,021 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 0.38 (14019 hom., cov: 35)
  • Exomes 𝑓: 0.31 (2 hom.)
• Consequence: PICSAR ENST00000615826.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615826.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PICSAR	NR_024089.2		n.664C>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PICSAR	ENST00000615826.2	TSL:1	n.690C>T		non_coding_transcript_exon	Exon 2 of 2
	PICSAR	ENST00000758108.1		n.628C>T		non_coding_transcript_exon	Exon 2 of 2
	PICSAR	ENST00000758109.1		n.1097C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57271 AN: 152032 Hom.: 13984 Cov.: 35

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.341

GnomAD4 exome AF: 0.308 AC: 8 AN: 26 Hom.: 2 Cov.: 0 AF XY: 0.389 AC XY: 7 AN XY: 18

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: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.318 AC: 7 AN: 22

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.377 AC: 57365 AN: 152150 Hom.: 14019 Cov.: 35 AF XY: 0.374 AC XY: 27819 AN XY: 74398

African (AFR) AF: 0.701 AC: 29059 AN: 41478

American (AMR) AF: 0.349 AC: 5345 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1716 AN: 5170

South Asian (SAS) AF: 0.204 AC: 982 AN: 4822

European-Finnish (FIN) AF: 0.241 AC: 2559 AN: 10606

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15915 AN: 67990

Other (OTH) AF: 0.344 AC: 726 AN: 2110

Alfa AF: 0.279 Hom.: 3665

Bravo AF: 0.404

Asia WGS AF: 0.303 AC: 1056 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs1557362; hg19: chr21-46419191;