Genetic Variant LINC01344:n.377-27419G>A (chr1-182231524-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000608183.1(LINC01344):n.118+11600G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,010 control chromosomes in the GnomAD database, including 3,891 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 0.21 ( 3891 hom., cov: 31)

Consequence

LINC01344
ENST00000608183.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.412

Publications

5 publications found

Variant links:

Genes affected

LINC01344 (HGNC:50554): (long intergenic non-protein coding RNA 1344)

LINC01344 links:

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new If you want to explore the variant's impact on the transcript ENST00000608183.1, 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608183.1. 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
	LINC01344	NR_104175.1		n.411-27419G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC01344	ENST00000420760.2	TSL:3	n.377-27419G>A	intron	N/A
LINC01344	ENST00000449842.2	TSL:3	n.411-27419G>A	intron	N/A
LINC01344	ENST00000608183.1	TSL:2	n.118+11600G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32261

AN:

151892

Hom.:

3891

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0851

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.384

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.235

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

GnomAD4 genome

AF:

0.212

AC:

32258

AN:

152010

Hom.:

3891

Cov.:

AF XY:

0.214

AC XY:

15900

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.0850

AC:

3525

AN:

41482

American (AMR)

AF:

0.266

AC:

4058

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

890

AN:

3472

East Asian (EAS)

AF:

0.385

AC:

1981

AN:

5152

South Asian (SAS)

AF:

0.254

AC:

1225

AN:

4816

European-Finnish (FIN)

AF:

0.211

AC:

2222

AN:

10548

Middle Eastern (MID)

AF:

0.327

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.259

AC:

17624

AN:

67974

Other (OTH)

AF:

0.235

AC:

496

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1256

2511

3767

5022

6278

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

350

700

1050

1400

1750

<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:

0.244

Hom.:

20408

Bravo

AF:

0.209

Asia WGS

AF:

0.265

AC:

921

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.1

(source)

DANN

Benign

0.63

PhyloP100

-0.41

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