chr21-45004592-G-T

Variant names:

• chr21-45004592-G-T
• rs13047060
• ENST00000615826.2:n.162C>A

Variant summary

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

The ENST00000615826.2(PICSAR):​n.162C>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 ENST00000615826.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• 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=-0.97).
• 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 rank	MANE	Protein	UniProt
PICSAR	NR_024089.2	n.136C>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PICSAR	ENST00000615826.2	n.162C>A		non_coding_transcript_exon_variant	Exon 1 of 2	1
PICSAR	ENST00000758108.1	n.112C>A		non_coding_transcript_exon_variant	Exon 1 of 2
PICSAR	ENST00000758109.1	n.24C>A		non_coding_transcript_exon_variant	Exon 1 of 3

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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.750 AC: 3 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 12 AN: 24

Middle Eastern (MID) AF: 1.00 AC: 4 AN: 4

European-Non Finnish (NFE) AF: 0.384 AC: 33 AN: 86

Other (OTH) AF: 0.500 AC: 4 AN: 8

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

African (AFR) AF: 0.162 AC: 6725 AN: 41488

American (AMR) AF: 0.617 AC: 9425 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1789 AN: 3466

East Asian (EAS) AF: 0.708 AC: 3645 AN: 5150

South Asian (SAS) AF: 0.654 AC: 3146 AN: 4812

European-Finnish (FIN) AF: 0.518 AC: 5471 AN: 10558

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.499 AC: 33874 AN: 67948

Other (OTH) AF: 0.477 AC: 1008 AN: 2112

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13047060; hg19: chr21-46424507;