Genetic Variant LINC00841:n.60T>G (chr10-43912449-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000446107.2(LINC00841):n.60T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,212 control chromosomes in the GnomAD database, including 26,639 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 0.59 ( 26586 hom., cov: 31)

Exomes 𝑓: 0.64 ( 53 hom. )

Consequence

LINC00841
ENST00000446107.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.48

Publications

3 publications found

Variant links:

Genes affected

LINC00841 (HGNC:27430): (long intergenic non-protein coding RNA 841)

LINC00841 links:

LINC02659 (HGNC:54145): (long intergenic non-protein coding RNA 2659)

LINC02659 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=-1.03).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00841	NR_136148.1 link	n.48T>G	non_coding_transcript_exon_variant	Exon 1 of 2
LINC00841	NR_033846.2 link	n.191+2790T>G	intron_variant	Intron 2 of 7
LINC00841	NR_136147.1 link	n.191+2790T>G	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00841	ENST00000446107.2 link	n.60T>G	non_coding_transcript_exon_variant	Exon 1 of 2	2
LINC00841	ENST00000826345.1 link	n.40T>G	non_coding_transcript_exon_variant	Exon 1 of 3
LINC00841	ENST00000826346.1 link	n.38T>G	non_coding_transcript_exon_variant	Exon 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.590

AC:

89623

AN:

151834

Hom.:

26569

Cov.:

show subpopulations

Gnomad AFR

AF:

0.532

Gnomad AMI

AF:

0.573

Gnomad AMR

AF:

0.544

Gnomad ASJ

AF:

0.645

Gnomad EAS

AF:

0.611

Gnomad SAS

AF:

0.693

Gnomad FIN

AF:

0.683

Gnomad MID

AF:

0.693

Gnomad NFE

AF:

0.609

Gnomad OTH

AF:

0.597

GnomAD4 exome

AF:

0.641

AC:

168

AN:

262

Hom.:

Cov.:

AF XY:

0.644

AC XY:

112

AN XY:

174

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.610

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.665

AC:

105

AN:

158

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.590

AC:

89667

AN:

151950

Hom.:

26586

Cov.:

AF XY:

0.595

AC XY:

44192

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.532

AC:

22026

AN:

41410

American (AMR)

AF:

0.543

AC:

8300

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.645

AC:

2240

AN:

3472

East Asian (EAS)

AF:

0.612

AC:

3148

AN:

5148

South Asian (SAS)

AF:

0.692

AC:

3334

AN:

4816

European-Finnish (FIN)

AF:

0.683

AC:

7222

AN:

10570

Middle Eastern (MID)

AF:

0.694

AC:

204

AN:

294

European-Non Finnish (NFE)

AF:

0.609

AC:

41403

AN:

67946

Other (OTH)

AF:

0.601

AC:

1267

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1920

3840

5761

7681

9601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

766

1532

2298

3064

3830

<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:

0.596

Hom.:

3373

Bravo

AF:

0.569

Asia WGS

AF:

0.651

AC:

2264

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.28

(source)

DANN

Benign

0.47

PhyloP100

-2.5

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