Genetic Variant ENST00000536495.1:n.57+1344G>T (chr11-61057137-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000536495.1(LINC02954):n.57+1344G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,966 control chromosomes in the GnomAD database, including 7,524 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 0.31 ( 7524 hom., cov: 32)

Consequence

LINC02954
ENST00000536495.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310

Publications

10 publications found

Variant links:

Genes affected

LINC02954 (HGNC:55972): (long intergenic non-protein coding RNA 2954)

LINC02954 links:

ENSG00000303405 (HGNC:):

ENSG00000303405 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 (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02954	NR_186234.1 link	n.231+1344G>T		intron_variant	Intron 2 of 3
LOC105369325	NR_188502.1 link	n.63-26742C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02954	ENST00000536495.1 link	n.57+1344G>T	intron_variant	Intron 1 of 3	3
LINC02954	ENST00000659437.1 link	n.206+1344G>T	intron_variant	Intron 2 of 3
LINC02954	ENST00000664141.1 link	n.402+1344G>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47354

AN:

151848

Hom.:

7517

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.395

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.333

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.333

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

GnomAD4 genome

AF:

0.312

AC:

47397

AN:

151966

Hom.:

7524

Cov.:

AF XY:

0.310

AC XY:

23001

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.329

AC:

13644

AN:

41440

American (AMR)

AF:

0.266

AC:

4073

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.252

AC:

873

AN:

3464

East Asian (EAS)

AF:

0.286

AC:

1480

AN:

5174

South Asian (SAS)

AF:

0.333

AC:

1607

AN:

4820

European-Finnish (FIN)

AF:

0.276

AC:

2913

AN:

10564

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.319

AC:

21662

AN:

67904

Other (OTH)

AF:

0.330

AC:

695

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1670

3340

5011

6681

8351

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<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:

0.313

Hom.:

14714

Bravo

AF:

0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.15

(source)

DANN

Benign

0.58

PhyloP100

0.031

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