dbSNP rs6078860: LINC01723:n.874+18880C>T (chr20-12986090-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000669657.1(LINC01723):n.874+18880C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 152,172 control chromosomes in the GnomAD database, including 441 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 0.063 ( 441 hom., cov: 32)

Consequence

LINC01723
ENST00000669657.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.283

Publications

1 publications found

Variant links:

Genes affected

LINC01723 (HGNC:52511): (long intergenic non-protein coding RNA 1723)

LINC01723 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.094 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01723	ENST00000669657.1 link	n.874+18880C>T	intron_variant	Intron 4 of 4
LINC01723	ENST00000670547.1 link	n.877-8820C>T	intron_variant	Intron 4 of 5
LINC01723	ENST00000671262.1 link	n.870+18880C>T	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.0629

AC:

9569

AN:

152054

Hom.:

441

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0154

Gnomad AMI

AF:

0.0626

Gnomad AMR

AF:

0.0535

Gnomad ASJ

AF:

0.0652

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0245

Gnomad FIN

AF:

0.0975

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0959

Gnomad OTH

AF:

0.0717

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

GnomAD4 genome

AF:

0.0629

AC:

9569

AN:

152172

Hom.:

441

Cov.:

AF XY:

0.0613

AC XY:

4561

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0153

AC:

637

AN:

41518

American (AMR)

AF:

0.0534

AC:

817

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0652

AC:

226

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5178

South Asian (SAS)

AF:

0.0247

AC:

119

AN:

4812

European-Finnish (FIN)

AF:

0.0975

AC:

1032

AN:

10590

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0959

AC:

6523

AN:

68000

Other (OTH)

AF:

0.0705

AC:

149

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

455

910

1365

1820

2275

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0885

Hom.:

280

Bravo

AF:

0.0565

Asia WGS

AF:

0.00924

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.9

(source)

DANN

Benign

0.39

PhyloP100

0.28

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