dbSNP rs17371334: LINC00333:n.139-104172T>G (chr13-84458192-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_046871.1(LINC00333):n.139-104172T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,046 control chromosomes in the GnomAD database, including 7,329 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 0.30 ( 7329 hom., cov: 33)

Consequence

LINC00333
NR_046871.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Publications

4 publications found

Variant links:

Genes affected

LINC00333 (HGNC:42050): (long intergenic non-protein coding RNA 333)

LINC00333 links:

LOC105370289 (HGNC:):

LOC105370289 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00333	NR_046871.1 link	n.139-104172T>G	intron_variant	Intron 3 of 6
LOC105370289	XR_942133.1 link	n.369-46273A>C	intron_variant	Intron 5 of 5
LOC105370289	XR_942134.1 link	n.366-46273A>C	intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

45997

AN:

151926

Hom.:

7323

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.578

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.321

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

GnomAD4 genome

AF:

0.303

AC:

46004

AN:

152046

Hom.:

7329

Cov.:

AF XY:

0.294

AC XY:

21843

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.250

AC:

10357

AN:

41472

American (AMR)

AF:

0.381

AC:

5808

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.411

AC:

1425

AN:

3468

East Asian (EAS)

AF:

0.124

AC:

639

AN:

5156

South Asian (SAS)

AF:

0.219

AC:

1057

AN:

4826

European-Finnish (FIN)

AF:

0.222

AC:

2344

AN:

10582

Middle Eastern (MID)

AF:

0.255

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.340

AC:

23105

AN:

67974

Other (OTH)

AF:

0.316

AC:

668

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1645

3291

4936

6582

8227

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

448

896

1344

1792

2240

<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:

0.331

Hom.:

34509

Bravo

AF:

0.315

Asia WGS

AF:

0.174

AC:

607

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.91

(source)

DANN

Benign

0.76

PhyloP100

-1.1

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