dbSNP rs1448539: LINC01117:n.398+49276T>C (chr2-176547071-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 ENST00000652995.1(LINC01117):n.398+49276T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,176 control chromosomes in the GnomAD database, including 49,526 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 0.80 ( 49526 hom., cov: 32)

Consequence

LINC01117
ENST00000652995.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.348

Publications

2 publications found

Variant links:

Genes affected

LINC01117 (HGNC:49260): (long intergenic non-protein coding RNA 1117)

LINC01117 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01117	ENST00000652995.1 link	n.398+49276T>C	intron_variant	Intron 2 of 3
LINC01117	ENST00000814385.1 link	n.185+51501T>C	intron_variant	Intron 2 of 4
LINC01117	ENST00000814386.1 link	n.245+51501T>C	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.798

AC:

121279

AN:

152058

Hom.:

49507

Cov.:

show subpopulations

Gnomad AFR

AF:

0.605

Gnomad AMI

AF:

0.942

Gnomad AMR

AF:

0.856

Gnomad ASJ

AF:

0.790

Gnomad EAS

AF:

0.935

Gnomad SAS

AF:

0.934

Gnomad FIN

AF:

0.892

Gnomad MID

AF:

0.801

Gnomad NFE

AF:

0.865

Gnomad OTH

AF:

0.798

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

GnomAD4 genome

AF:

0.797

AC:

121341

AN:

152176

Hom.:

49526

Cov.:

AF XY:

0.803

AC XY:

59742

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.605

AC:

25077

AN:

41478

American (AMR)

AF:

0.856

AC:

13094

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.790

AC:

2742

AN:

3470

East Asian (EAS)

AF:

0.936

AC:

4846

AN:

5180

South Asian (SAS)

AF:

0.934

AC:

4495

AN:

4814

European-Finnish (FIN)

AF:

0.892

AC:

9453

AN:

10598

Middle Eastern (MID)

AF:

0.803

AC:

236

AN:

294

European-Non Finnish (NFE)

AF:

0.865

AC:

58850

AN:

68018

Other (OTH)

AF:

0.798

AC:

1689

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1180

2360

3540

4720

5900

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

868

1736

2604

3472

4340

<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:

0.852

Hom.:

27971

Bravo

AF:

0.784

Asia WGS

AF:

0.872

AC:

3033

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

7.7

(source)

DANN

Benign

0.73

PhyloP100

0.35

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