dbSNP rs2150392: LINC00161:n.645C>A (chr21-28540130-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000412526.5(LINC00161):n.645C>A 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 0.501 in 151,922 control chromosomes in the GnomAD database, including 22,528 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 0.50 ( 22526 hom., cov: 31)

Exomes 𝑓: 0.83 ( 2 hom. )

Consequence

LINC00161
ENST00000412526.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.850

Publications

7 publications found

Variant links:

Genes affected

LINC00161 (HGNC:17138): (long intergenic non-protein coding RNA 161)

LINC00161 links:

LINC03138 (HGNC:58104):

LINC03138 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000412526.5, 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412526.5. 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
	LINC00161	NR_026552.2		n.645C>A		non_coding_transcript_exon	Exon 2 of 2
	LINC00161	NR_026553.2		n.289C>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC00161	ENST00000412526.5	TSL:2	n.645C>A	non_coding_transcript_exon	Exon 2 of 2
LINC00161	ENST00000455939.1	TSL:2	n.289C>A	non_coding_transcript_exon	Exon 2 of 2
LINC00161	ENST00000825125.1		n.340C>A	non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.502

AC:

76133

AN:

151798

Hom.:

22530

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.667

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.591

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.734

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.543

GnomAD4 exome

AF:

0.833

AC:

AN:

Hom.:

Cov.:

AF XY:

0.833

AC XY:

AN XY:

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.833

AC:

AN:

Other (OTH)

AC:

AN:

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.275

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.501

AC:

76129

AN:

151916

Hom.:

22526

Cov.:

AF XY:

0.502

AC XY:

37282

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.208

AC:

8617

AN:

41424

American (AMR)

AF:

0.486

AC:

7414

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.591

AC:

2048

AN:

3468

East Asian (EAS)

AF:

0.182

AC:

940

AN:

5154

South Asian (SAS)

AF:

0.476

AC:

2290

AN:

4808

European-Finnish (FIN)

AF:

0.734

AC:

7740

AN:

10546

Middle Eastern (MID)

AF:

0.551

AC:

162

AN:

294

European-Non Finnish (NFE)

AF:

0.665

AC:

45185

AN:

67964

Other (OTH)

AF:

0.538

AC:

1129

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1589

3179

4768

6358

7947

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<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:

0.598

Hom.:

14729

Bravo

AF:

0.469

Asia WGS

AF:

0.280

AC:

978

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.67

(source)

DANN

Benign

0.82

PhyloP100

-0.85

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