dbSNP rs6982990: LINC01606:n.224-203A>G (chr8-57202716-A-G) – 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.224-203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 151,792 control chromosomes in the GnomAD database, including 2,669 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 0.17 ( 2669 hom., cov: 32)

Consequence

LINC01606
ENST00000518556.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66

Publications

2 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=-1.06).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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.224-203A>G	intron_variant	Intron 2 of 2	3
LINC01606	ENST00000519241.6 link	n.558+8705A>G	intron_variant	Intron 4 of 8	3
LINC01606	ENST00000521653.6 link	n.228-5293A>G	intron_variant	Intron 2 of 6	4

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26420

AN:

151672

Hom.:

2650

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.0803

Gnomad FIN

AF:

0.168

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.161

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

GnomAD4 genome

AF:

0.174

AC:

26477

AN:

151792

Hom.:

2669

Cov.:

AF XY:

0.173

AC XY:

12844

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.286

AC:

11835

AN:

41374

American (AMR)

AF:

0.129

AC:

1971

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

356

AN:

3468

East Asian (EAS)

AF:

0.138

AC:

707

AN:

5116

South Asian (SAS)

AF:

0.0802

AC:

385

AN:

4800

European-Finnish (FIN)

AF:

0.168

AC:

1771

AN:

10528

Middle Eastern (MID)

AF:

0.132

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.133

AC:

9020

AN:

67956

Other (OTH)

AF:

0.161

AC:

339

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1087

2175

3262

4350

5437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

276

552

828

1104

1380

<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:

0.161

Hom.:

273

Bravo

AF:

0.177

Asia WGS

AF:

0.120

AC:

416

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

2.7

(source)

DANN

Benign

0.13

PhyloP100

-1.7

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