Genetic Variant ENST00000519691.2:n.1076C>T (chr8-37598786-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 ENST00000519691.2(LINC01605):n.1076C>T 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 0.0922 in 268,786 control chromosomes in the GnomAD database, including 1,439 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 0.083 ( 683 hom., cov: 32)

Exomes 𝑓: 0.10 ( 756 hom. )

Consequence

LINC01605
ENST00000519691.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

3 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=-0.79).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01605	NR_170186.1 link	n.779+275C>T	intron_variant	Intron 1 of 4
LINC01605	NR_170187.1 link	n.779+275C>T	intron_variant	Intron 1 of 6
LINC01605	NR_170188.1 link	n.779+275C>T	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01605	ENST00000519691.2 link	n.1076C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC01605	ENST00000784554.1 link	n.194C>T	non_coding_transcript_exon_variant	Exon 2 of 2
LINC01605	ENST00000517363.2 link	n.34+275C>T	intron_variant	Intron 1 of 7	3

Frequencies

GnomAD3 genomes

AF:

0.0830

AC:

12619

AN:

152108

Hom.:

682

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0213

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.0768

Gnomad ASJ

AF:

0.0845

Gnomad EAS

AF:

0.0667

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.102

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.0809

GnomAD4 exome

AF:

0.104

AC:

12167

AN:

116560

Hom.:

756

Cov.:

AF XY:

0.110

AC XY:

6915

AN XY:

63026

show subpopulations

African (AFR)

AF:

0.0177

AC:

AN:

1642

American (AMR)

AF:

0.0615

AC:

257

AN:

4180

Ashkenazi Jewish (ASJ)

AF:

0.0742

AC:

200

AN:

2696

East Asian (EAS)

AF:

0.0396

AC:

AN:

1842

South Asian (SAS)

AF:

0.152

AC:

3550

AN:

23284

European-Finnish (FIN)

AF:

0.123

AC:

753

AN:

6112

Middle Eastern (MID)

AF:

0.0942

AC:

AN:

446

European-Non Finnish (NFE)

AF:

0.0952

AC:

6708

AN:

70476

Other (OTH)

AF:

0.0944

AC:

555

AN:

5882

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

498

996

1493

1991

2489

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

138

184

230

<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:

0.0829

AC:

12613

AN:

152226

Hom.:

683

Cov.:

AF XY:

0.0858

AC XY:

6386

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0212

AC:

882

AN:

41546

American (AMR)

AF:

0.0767

AC:

1173

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0845

AC:

293

AN:

3468

East Asian (EAS)

AF:

0.0670

AC:

347

AN:

5176

South Asian (SAS)

AF:

0.185

AC:

893

AN:

4822

European-Finnish (FIN)

AF:

0.133

AC:

1406

AN:

10596

Middle Eastern (MID)

AF:

0.0959

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.106

AC:

7214

AN:

68006

Other (OTH)

AF:

0.0800

AC:

169

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

593

1185

1778

2370

2963

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.0966

Hom.:

1283

Bravo

AF:

0.0735

Asia WGS

AF:

0.134

AC:

464

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.3

(source)

DANN

Benign

0.76

PhyloP100

-1.1

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