dbSNP rs12195826: LINC01600:n.62-1289T>C (chr6-2565518-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 ENST00000840975.1(LINC01600):n.62-1289T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,072 control chromosomes in the GnomAD database, including 30,330 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 0.63 ( 30330 hom., cov: 31)

Consequence

LINC01600
ENST00000840975.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.971

Publications

9 publications found

Variant links:

Genes affected

LINC01600 (HGNC:21600): (long intergenic non-protein coding RNA 1600)

LINC01600 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01600	ENST00000840975.1 link	n.62-1289T>C		intron_variant	Intron 1 of 1
LINC01600	ENST00000840976.1 link	n.359-1289T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.630

AC:

95732

AN:

151954

Hom.:

30315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.572

Gnomad AMI

AF:

0.664

Gnomad AMR

AF:

0.618

Gnomad ASJ

AF:

0.617

Gnomad EAS

AF:

0.545

Gnomad SAS

AF:

0.589

Gnomad FIN

AF:

0.683

Gnomad MID

AF:

0.582

Gnomad NFE

AF:

0.670

Gnomad OTH

AF:

0.608

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

GnomAD4 genome

AF:

0.630

AC:

95789

AN:

152072

Hom.:

30330

Cov.:

AF XY:

0.627

AC XY:

46591

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.572

AC:

23727

AN:

41486

American (AMR)

AF:

0.618

AC:

9440

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.617

AC:

2140

AN:

3468

East Asian (EAS)

AF:

0.544

AC:

2808

AN:

5166

South Asian (SAS)

AF:

0.590

AC:

2847

AN:

4828

European-Finnish (FIN)

AF:

0.683

AC:

7213

AN:

10558

Middle Eastern (MID)

AF:

0.585

AC:

172

AN:

294

European-Non Finnish (NFE)

AF:

0.670

AC:

45562

AN:

67974

Other (OTH)

AF:

0.605

AC:

1277

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1844

3688

5533

7377

9221

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.641

Hom.:

52959

Bravo

AF:

0.620

Asia WGS

AF:

0.550

AC:

1912

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.96

(source)

DANN

Benign

0.49

PhyloP100

-0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs12195826

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