dbSNP rs10501861: LINC02737:n.124-59856A>C (chr11-96599737-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 ENST00000716805.1(LINC02737):n.124-59856A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.014 in 152,078 control chromosomes in the GnomAD database, including 53 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 0.014 ( 53 hom., cov: 31)

Consequence

LINC02737
ENST00000716805.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.147

Publications

0 publications found

Variant links:

Genes affected

LINC02737 (HGNC:54254): (long intergenic non-protein coding RNA 2737)

LINC02737 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02737	ENST00000716805.1 link	n.124-59856A>C	intron_variant	Intron 2 of 6
LINC02737	ENST00000716807.1 link	n.352+11504A>C	intron_variant	Intron 3 of 5
LINC02737	ENST00000716808.1 link	n.158+9263A>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0140

AC:

2128

AN:

151960

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00940

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0471

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.0579

Gnomad SAS

AF:

0.0263

Gnomad FIN

AF:

0.0101

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00632

Gnomad OTH

AF:

0.0163

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

GnomAD4 genome

AF:

0.0140

AC:

2135

AN:

152078

Hom.:

Cov.:

AF XY:

0.0149

AC XY:

1109

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.00954

AC:

396

AN:

41498

American (AMR)

AF:

0.0476

AC:

726

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.00519

AC:

AN:

3470

East Asian (EAS)

AF:

0.0575

AC:

296

AN:

5152

South Asian (SAS)

AF:

0.0253

AC:

122

AN:

4826

European-Finnish (FIN)

AF:

0.0101

AC:

107

AN:

10574

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00632

AC:

430

AN:

67986

Other (OTH)

AF:

0.0161

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

105

211

316

422

527

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00942

Hom.:

Bravo

AF:

0.0170

Asia WGS

AF:

0.0460

AC:

161

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.5

(source)

DANN

Benign

0.72

PhyloP100

0.15

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs10501861

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