dbSNP rs2318144: LINC01606:n.224-735G>A (chr8-57202184-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 ENST00000518556.5(LINC01606):n.224-735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,170 control chromosomes in the GnomAD database, including 994 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 ( 994 hom., cov: 32)

Consequence

LINC01606
ENST00000518556.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.326

Publications

7 publications found

Variant links:

Genes affected

LINC01606 (HGNC:51656): (long intergenic non-protein coding RNA 1606)

LINC01606 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 (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01606	ENST00000518556.5 link	n.224-735G>A	intron_variant	Intron 2 of 2	3
LINC01606	ENST00000519241.6 link	n.558+8173G>A	intron_variant	Intron 4 of 8	3
LINC01606	ENST00000521653.6 link	n.228-5825G>A	intron_variant	Intron 2 of 6	4

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

17088

AN:

152052

Hom.:

989

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0797

Gnomad AMI

AF:

0.0604

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.0971

Gnomad EAS

AF:

0.137

Gnomad SAS

AF:

0.0725

Gnomad FIN

AF:

0.166

Gnomad MID

AF:

0.0987

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.112

AC:

17110

AN:

152170

Hom.:

994

Cov.:

AF XY:

0.112

AC XY:

8353

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0800

AC:

3322

AN:

41540

American (AMR)

AF:

0.103

AC:

1569

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0971

AC:

337

AN:

3470

East Asian (EAS)

AF:

0.137

AC:

707

AN:

5142

South Asian (SAS)

AF:

0.0723

AC:

349

AN:

4826

European-Finnish (FIN)

AF:

0.166

AC:

1758

AN:

10588

Middle Eastern (MID)

AF:

0.103

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.129

AC:

8745

AN:

68008

Other (OTH)

AF:

0.113

AC:

238

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

789

1577

2366

3154

3943

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

392

588

784

980

<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:

0.126

Hom.:

1256

Bravo

AF:

0.109

Asia WGS

AF:

0.102

AC:

352

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

2.1

(source)

DANN

Benign

0.35

PhyloP100

0.33

Mutation Taster

=100/0

polymorphism (auto)

(source)

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