dbSNP rs6589076: LINC02715:n.409-51208C>T (chr11-109634851-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000818760.1(LINC02715):n.409-51208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,068 control chromosomes in the GnomAD database, including 1,193 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 0.11 ( 1193 hom., cov: 32)

Consequence

LINC02715
ENST00000818760.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.830

Publications

1 publications found

Variant links:

Genes affected

LINC02715 (HGNC:54232): (long intergenic non-protein coding RNA 2715)

LINC02715 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02715	ENST00000818760.1 link	n.409-51208C>T	intron_variant	Intron 3 of 9
LINC02715	ENST00000818761.1 link	n.170-122126C>T	intron_variant	Intron 2 of 3
LINC02715	ENST00000818762.1 link	n.148-122126C>T	intron_variant	Intron 2 of 3
LINC02715	ENST00000818763.1 link	n.79-51208C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15978

AN:

151950

Hom.:

1186

Cov.:

show subpopulations

Gnomad AFR

AF:

0.204

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.0825

Gnomad ASJ

AF:

0.0712

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0449

Gnomad FIN

AF:

0.0307

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0765

Gnomad OTH

AF:

0.102

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

GnomAD4 genome

AF:

0.105

AC:

16008

AN:

152068

Hom.:

1193

Cov.:

AF XY:

0.101

AC XY:

7537

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.204

AC:

8469

AN:

41450

American (AMR)

AF:

0.0823

AC:

1259

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0712

AC:

247

AN:

3470

East Asian (EAS)

AF:

0.00154

AC:

AN:

5180

South Asian (SAS)

AF:

0.0445

AC:

215

AN:

4828

European-Finnish (FIN)

AF:

0.0307

AC:

323

AN:

10526

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0765

AC:

5201

AN:

68004

Other (OTH)

AF:

0.101

AC:

214

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

687

1374

2062

2749

3436

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

162

324

486

648

810

<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:

0.0939

Hom.:

119

Bravo

AF:

0.114

Asia WGS

AF:

0.0390

AC:

136

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

-0.83

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