rs881969

Variant names:

• chr21-45001779-G-A
• rs881969
• ENST00000615826.2:n.311-2123C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-45001779-G-A
• chr21-45001779-G-C
• chr21-45001779-G-T

Variant summary

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

The ENST00000615826.2(PICSAR):​n.311-2123C>T variant causes a intron 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 ENST00000615826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 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.285-2123C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PICSAR	ENST00000615826.2	TSL:1	n.311-2123C>T		intron	N/A
	PICSAR	ENST00000758108.1		n.249-2123C>T		intron	N/A
	PICSAR	ENST00000758109.1		n.173-1171C>T		intron	N/A

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

African (AFR) AF: 0.0786 AC: 3263 AN: 41508

American (AMR) AF: 0.149 AC: 2281 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3468

East Asian (EAS) AF: 0.170 AC: 864 AN: 5094

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4818

European-Finnish (FIN) AF: 0.193 AC: 2050 AN: 10600

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15470 AN: 67910

Other (OTH) AF: 0.189 AC: 400 AN: 2112

Alfa AF: 0.216 Hom.: 6975

Bravo AF: 0.166

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.074
DANN	Benign	0.66
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs881969; hg19: chr21-46421694;