dbSNP rs16935279: LINC01592:n.416-7055A>G (chr8-68961217-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 ENST00000518540.5(LINC01592):n.416-7055A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 152,292 control chromosomes in the GnomAD database, including 163 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 0.022 ( 163 hom., cov: 32)

Consequence

LINC01592
ENST00000518540.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.413

Publications

5 publications found

Variant links:

Genes affected

LINC01592 (HGNC:51557): (long intergenic non-protein coding RNA 1592)

LINC01592 links:

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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=-0.68).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01592	NR_039986.1 link	n.416-7055A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01592	ENST00000518540.5 link	n.416-7055A>G	intron_variant	Intron 2 of 4	2
LINC01592	ENST00000519062.7 link	n.150-7104A>G	intron_variant	Intron 1 of 3	3
LINC01592	ENST00000524286.2 link	n.167-7104A>G	intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.0224

AC:

3408

AN:

152174

Hom.:

165

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00519

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0159

Gnomad ASJ

AF:

0.0265

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.0336

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0116

Gnomad OTH

AF:

0.0239

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

GnomAD4 genome

AF:

0.0224

AC:

3407

AN:

152292

Hom.:

163

Cov.:

AF XY:

0.0255

AC XY:

1902

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.00522

AC:

217

AN:

41584

American (AMR)

AF:

0.0161

AC:

246

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0265

AC:

AN:

3468

East Asian (EAS)

AF:

0.220

AC:

1134

AN:

5166

South Asian (SAS)

AF:

0.105

AC:

504

AN:

4822

European-Finnish (FIN)

AF:

0.0336

AC:

357

AN:

10618

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0116

AC:

787

AN:

68028

Other (OTH)

AF:

0.0250

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

155

309

464

618

773

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0148

Hom.:

Bravo

AF:

0.0192

Asia WGS

AF:

0.152

AC:

526

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

9.6

(source)

DANN

Benign

0.93

PhyloP100

0.41

Splicing

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

Publications

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rs16935279

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