rs1557361

Variant names:

• chr21-44998900-T-C
• rs1557361
• ENST00000615826.2:n.*240A>G

Your query was ambiguous. Multiple possible variants found:

• chr21-44998900-T-C
• chr21-44998900-T-G

Variant summary

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

The ENST00000615826.2(PICSAR):​n.*240A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,152 control chromosomes in the GnomAD database, including 13,085 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 0.37 (13085 hom., cov: 35)
• Consequence: PICSAR ENST00000615826.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PICSAR	ENST00000615826.2	n.*240A>G		downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55841 AN: 152034 Hom.: 13059 Cov.: 35

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.368 AC: 55922 AN: 152152 Hom.: 13085 Cov.: 35 AF XY: 0.365 AC XY: 27142 AN XY: 74386

African (AFR) AF: 0.668 AC: 27706 AN: 41488

American (AMR) AF: 0.345 AC: 5287 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3472

East Asian (EAS) AF: 0.333 AC: 1712 AN: 5148

South Asian (SAS) AF: 0.203 AC: 981 AN: 4828

European-Finnish (FIN) AF: 0.241 AC: 2553 AN: 10606

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15905 AN: 67980

Other (OTH) AF: 0.340 AC: 718 AN: 2114

Alfa AF: 0.309 Hom.: 1189

Bravo AF: 0.394

Asia WGS AF: 0.304 AC: 1060 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	3.1
DANN	Benign	0.29
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1557361; hg19: chr21-46418814;