Genetic Variant ENST00000472821.6:n.161-8181C>T (chr3-150116757-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000472821.6(LINC01213):n.161-8181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 152,078 control chromosomes in the GnomAD database, including 672 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 0.082 ( 672 hom., cov: 32)

Consequence

LINC01213
ENST00000472821.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0580

Publications

4 publications found

Variant links:

Genes affected

LINC01213 (HGNC:49648): (long intergenic non-protein coding RNA 1213)

LINC01213 links:

LOC105374313 (HGNC:):

LOC105374313 links:

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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 (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374313	NR_136187.1 link	n.156-8181C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01213	ENST00000472821.6 link	n.161-8181C>T	intron_variant	Intron 1 of 2	3
LINC01213	ENST00000487840.6 link	n.99-8181C>T	intron_variant	Intron 1 of 2	2
LINC01213	ENST00000489690.1 link	n.120-8181C>T	intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.0819

AC:

12445

AN:

151960

Hom.:

670

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0517

Gnomad ASJ

AF:

0.0697

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.0489

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0513

Gnomad OTH

AF:

0.0655

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

GnomAD4 genome

AF:

0.0820

AC:

12465

AN:

152078

Hom.:

672

Cov.:

AF XY:

0.0824

AC XY:

6129

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.141

AC:

5846

AN:

41444

American (AMR)

AF:

0.0516

AC:

788

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0697

AC:

242

AN:

3472

East Asian (EAS)

AF:

0.155

AC:

799

AN:

5166

South Asian (SAS)

AF:

0.126

AC:

607

AN:

4804

European-Finnish (FIN)

AF:

0.0489

AC:

519

AN:

10610

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0513

AC:

3487

AN:

67994

Other (OTH)

AF:

0.0695

AC:

147

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

575

1150

1726

2301

2876

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0593

Hom.:

931

Bravo

AF:

0.0831

Asia WGS

AF:

0.148

AC:

517

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

3.1

(source)

DANN

Benign

0.71

PhyloP100

0.058

Splicing

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

Publications

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ENST00000472821.6:n.161-8181C>T

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