dbSNP rs10837766: LINC02745:n.342-12585A>G (chr11-42006251-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 ENST00000527828.6(LINC02745):n.342-12585A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,094 control chromosomes in the GnomAD database, including 1,650 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 0.14 ( 1650 hom., cov: 32)

Consequence

LINC02745
ENST00000527828.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0620

Publications

3 publications found

Variant links:

Genes affected

LINC02745 (HGNC:54263): (long intergenic non-protein coding RNA 2745)

LINC02745 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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02745	NR_135065.1 link	n.1065-167A>G		intron_variant	Intron 8 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02745	ENST00000527828.6 link	n.342-12585A>G	intron_variant	Intron 3 of 3	3
LINC02745	ENST00000663570.1 link	n.800-12585A>G	intron_variant	Intron 6 of 6
LINC02745	ENST00000667585.1 link	n.361-12585A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22029

AN:

151976

Hom.:

1650

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.141

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.135

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

GnomAD4 genome

AF:

0.145

AC:

22051

AN:

152094

Hom.:

1650

Cov.:

AF XY:

0.143

AC XY:

10641

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.150

AC:

6238

AN:

41498

American (AMR)

AF:

0.107

AC:

1626

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

407

AN:

3470

East Asian (EAS)

AF:

0.141

AC:

729

AN:

5176

South Asian (SAS)

AF:

0.157

AC:

756

AN:

4822

European-Finnish (FIN)

AF:

0.134

AC:

1424

AN:

10592

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.153

AC:

10432

AN:

67980

Other (OTH)

AF:

0.133

AC:

281

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

930

1860

2791

3721

4651

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.144

Hom.:

1255

Bravo

AF:

0.145

Asia WGS

AF:

0.158

AC:

546

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.5

(source)

DANN

Benign

0.51

PhyloP100

0.062

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