Genetic Variant LINC02194:n.34-4201A>G (chr16-24243631-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000567127.1(LINC02194):n.34-4201A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,986 control chromosomes in the GnomAD database, including 34,492 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 0.67 ( 34492 hom., cov: 31)

Consequence

LINC02194
ENST00000567127.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0600

Publications

4 publications found

Variant links:

Genes affected

LINC02194 (HGNC:53057): (long intergenic non-protein coding RNA 2194)

LINC02194 links:

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new If you want to explore the variant's impact on the transcript ENST00000567127.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567127.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02194	NR_146569.1		n.34-4201A>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC02194	ENST00000567127.1	TSL:3	n.34-4201A>G	intron	N/A
LINC02194	ENST00000567624.1	TSL:3	n.53-3461A>G	intron	N/A
LINC02194	ENST00000747929.1		n.237-4201A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.668

AC:

101397

AN:

151868

Hom.:

34462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.798

Gnomad AMI

AF:

0.515

Gnomad AMR

AF:

0.551

Gnomad ASJ

AF:

0.715

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.648

Gnomad FIN

AF:

0.578

Gnomad MID

AF:

0.670

Gnomad NFE

AF:

0.638

Gnomad OTH

AF:

0.669

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

GnomAD4 genome

AF:

0.668

AC:

101471

AN:

151986

Hom.:

34492

Cov.:

AF XY:

0.664

AC XY:

49321

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.798

AC:

33066

AN:

41450

American (AMR)

AF:

0.550

AC:

8394

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.715

AC:

2479

AN:

3468

East Asian (EAS)

AF:

0.554

AC:

2853

AN:

5154

South Asian (SAS)

AF:

0.649

AC:

3123

AN:

4814

European-Finnish (FIN)

AF:

0.578

AC:

6100

AN:

10556

Middle Eastern (MID)

AF:

0.666

AC:

193

AN:

290

European-Non Finnish (NFE)

AF:

0.638

AC:

43386

AN:

67966

Other (OTH)

AF:

0.666

AC:

1407

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1685

3370

5055

6740

8425

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.646

Hom.:

41606

Bravo

AF:

0.668

Asia WGS

AF:

0.590

AC:

2053

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.6

(source)

DANN

Benign

0.50

PhyloP100

-0.060

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over