rs7277744

Variant names:

• chr21-45004654-C-T
• rs7277744
• ENST00000615826.2:n.100G>A

Variant summary

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

The ENST00000615826.2(PICSAR):​n.100G>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 152,040 control chromosomes in the GnomAD database, including 16,078 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 (16073 hom., cov: 31)
  • Exomes 𝑓: 0.55 (5 hom.)
• Consequence: PICSAR ENST00000615826.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989
• 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=-0.94).
• 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.74G>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.100G>A		non_coding_transcript_exon_variant	Exon 1 of 2	1
PICSAR	ENST00000758108.1	n.50G>A		non_coding_transcript_exon_variant	Exon 1 of 2
PICSAR	ENST00000758109.1	n.-39G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65522 AN: 151884 Hom.: 16060 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.474

GnomAD4 exome AF: 0.553 AC: 21 AN: 38 Hom.: 5 Cov.: 0 AF XY: 0.625 AC XY: 20 AN XY: 32

African (AFR) AF: 1.00 AC: 2 AN: 2

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

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: 0.400 AC: 4 AN: 10

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.550 AC: 11 AN: 20

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.431 AC: 65562 AN: 152002 Hom.: 16073 Cov.: 31 AF XY: 0.441 AC XY: 32782 AN XY: 74288

African (AFR) AF: 0.197 AC: 8151 AN: 41474

American (AMR) AF: 0.611 AC: 9333 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1723 AN: 3472

East Asian (EAS) AF: 0.709 AC: 3644 AN: 5142

South Asian (SAS) AF: 0.656 AC: 3155 AN: 4806

European-Finnish (FIN) AF: 0.502 AC: 5301 AN: 10566

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32786 AN: 67950

Other (OTH) AF: 0.474 AC: 1002 AN: 2114

Alfa AF: 0.469 Hom.: 8510

Bravo AF: 0.428

Asia WGS AF: 0.644 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs7277744; hg19: chr21-46424569;