21-45001779-G-A

Position:

• chr21-45001779-G-A

Variant summary

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

The NR_024089.2(PICSAR):​n.285-2123C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,016 control chromosomes in the GnomAD database, including 2,813 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 0.18 (2813 hom., cov: 31)
• Consequence: PICSAR NR_024089.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PICSAR	NR_024089.2	n.285-2123C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PICSAR	ENST00000615826.1	n.285-2123C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26872 AN: 151900 Hom.: 2819 Cov.: 31

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.193

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.177 AC: 26859 AN: 152016 Hom.: 2813 Cov.: 31 AF XY: 0.176 AC XY: 13089 AN XY: 74308

Gnomad4 AFR AF: 0.0786

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.189

Alfa AF: 0.222 Hom.: 4683

Bravo AF: 0.166

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.074
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs881969; hg19: chr21-46421694;