dbSNP rs2298320: LINC01605:n.942T>C (chr8-37598920-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 ENST00000519691.2(LINC01605):n.942T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 166,452 control chromosomes in the GnomAD database, including 18,148 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 0.47 ( 16817 hom., cov: 32)

Exomes 𝑓: 0.41 ( 1331 hom. )

Consequence

LINC01605
ENST00000519691.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.231

Publications

1 publications found

Variant links:

Genes affected

LINC01605 (HGNC:51654): (long intergenic non-protein coding RNA 1605)

LINC01605 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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01605	NR_170186.1 link	n.779+141T>C	intron_variant	Intron 1 of 4
LINC01605	NR_170187.1 link	n.779+141T>C	intron_variant	Intron 1 of 6
LINC01605	NR_170188.1 link	n.779+141T>C	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01605	ENST00000519691.2 link	n.942T>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC01605	ENST00000784554.1 link	n.60T>C	non_coding_transcript_exon_variant	Exon 2 of 2
LINC01605	ENST00000517363.2 link	n.34+141T>C	intron_variant	Intron 1 of 7	3

Frequencies

GnomAD3 genomes

AF:

0.466

AC:

70868

AN:

151928

Hom.:

16783

Cov.:

show subpopulations

Gnomad AFR

AF:

0.402

Gnomad AMI

AF:

0.548

Gnomad AMR

AF:

0.486

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.466

Gnomad SAS

AF:

0.492

Gnomad FIN

AF:

0.562

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.487

Gnomad OTH

AF:

0.462

GnomAD4 exome

AF:

0.412

AC:

5940

AN:

14406

Hom.:

1331

Cov.:

AF XY:

0.417

AC XY:

3048

AN XY:

7308

show subpopulations

African (AFR)

AF:

0.315

AC:

AN:

American (AMR)

AF:

0.397

AC:

516

AN:

1300

Ashkenazi Jewish (ASJ)

AF:

0.368

AC:

103

AN:

280

East Asian (EAS)

AF:

0.431

AC:

AN:

102

South Asian (SAS)

AF:

0.367

AC:

581

AN:

1582

European-Finnish (FIN)

AF:

0.488

AC:

281

AN:

576

Middle Eastern (MID)

AF:

0.407

AC:

AN:

European-Non Finnish (NFE)

AF:

0.421

AC:

4036

AN:

9582

Other (OTH)

AF:

0.391

AC:

328

AN:

838

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

158

315

473

630

788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.467

AC:

70962

AN:

152046

Hom.:

16817

Cov.:

AF XY:

0.473

AC XY:

35144

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.403

AC:

16716

AN:

41480

American (AMR)

AF:

0.486

AC:

7434

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.411

AC:

1428

AN:

3472

East Asian (EAS)

AF:

0.467

AC:

2404

AN:

5152

South Asian (SAS)

AF:

0.493

AC:

2377

AN:

4824

European-Finnish (FIN)

AF:

0.562

AC:

5933

AN:

10560

Middle Eastern (MID)

AF:

0.398

AC:

117

AN:

294

European-Non Finnish (NFE)

AF:

0.487

AC:

33076

AN:

67960

Other (OTH)

AF:

0.463

AC:

977

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1949

3898

5846

7795

9744

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<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:

0.473

Hom.:

5632

Bravo

AF:

0.457

Asia WGS

AF:

0.469

AC:

1631

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.83

(source)

DANN

Benign

0.60

PhyloP100

-0.23

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over