dbSNP rs9646096: LINC01048:n.103-6916T>G (chr13-37491309-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000827904.1(LINC01048):n.103-6916T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0503 in 152,258 control chromosomes in the GnomAD database, including 237 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 0.050 ( 237 hom., cov: 32)

Consequence

LINC01048
ENST00000827904.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.970

Publications

9 publications found

Variant links:

Genes affected

LINC01048 (HGNC:49042): (long intergenic non-protein coding RNA 1048)

LINC01048 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0797 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
LINC01048	ENST00000827904.1 link	n.103-6916T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0502

AC:

7640

AN:

152140

Hom.:

235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0572

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0831

Gnomad ASJ

AF:

0.0551

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0172

Gnomad FIN

AF:

0.0426

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0454

Gnomad OTH

AF:

0.0694

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

GnomAD4 genome

AF:

0.0503

AC:

7656

AN:

152258

Hom.:

237

Cov.:

AF XY:

0.0501

AC XY:

3729

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.0572

AC:

2380

AN:

41574

American (AMR)

AF:

0.0835

AC:

1275

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.0551

AC:

191

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5176

South Asian (SAS)

AF:

0.0178

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0426

AC:

452

AN:

10606

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0454

AC:

3086

AN:

68020

Other (OTH)

AF:

0.0687

AC:

145

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

374

748

1121

1495

1869

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<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:

0.0454

Hom.:

105

Bravo

AF:

0.0531

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

8.5

(source)

DANN

Benign

0.63

PhyloP100

0.97

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