dbSNP rs36221778: PICSAR:n.22A>G (chr21-45004732-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000615826.2(PICSAR):n.22A>G 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 0.0898 in 152,194 control chromosomes in the GnomAD database, including 757 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 0.090 ( 757 hom., cov: 32)

Exomes 𝑓: 0.050 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PICSAR
ENST00000615826.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.275

Publications

2 publications found

Variant links:

Genes affected

PICSAR (HGNC:19725): (P38 inhibited cutaneous squamous cell carcinoma associated lincRNA)

PICSAR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PICSAR	NR_024089.2 link	n.-5A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PICSAR	ENST00000615826.2 link	n.22A>G	non_coding_transcript_exon_variant	Exon 1 of 2	1
PICSAR	ENST00000758108.1 link	n.-29A>G	upstream_gene_variant
PICSAR	ENST00000758109.1 link	n.-117A>G	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0898

AC:

13664

AN:

152076

Hom.:

756

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.0622

Gnomad ASJ

AF:

0.0678

Gnomad EAS

AF:

0.100

Gnomad SAS

AF:

0.0271

Gnomad FIN

AF:

0.0787

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0627

Gnomad OTH

AF:

0.0703

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0898

AC:

13674

AN:

152194

Hom.:

757

Cov.:

AF XY:

0.0891

AC XY:

6633

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.155

AC:

6419

AN:

41514

American (AMR)

AF:

0.0621

AC:

950

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0678

AC:

235

AN:

3466

East Asian (EAS)

AF:

0.100

AC:

516

AN:

5156

South Asian (SAS)

AF:

0.0268

AC:

129

AN:

4822

European-Finnish (FIN)

AF:

0.0787

AC:

835

AN:

10610

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0626

AC:

4258

AN:

68002

Other (OTH)

AF:

0.0728

AC:

154

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

641

1281

1922

2562

3203

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0816

Hom.:

Bravo

AF:

0.0928

Asia WGS

AF:

0.0740

AC:

260

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.1

(source)

DANN

Benign

0.39

PhyloP100

0.28

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over