dbSNP rs6750795: LINC00471:n.407+7A>G (chr2-231513520-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000313064.5(LINC00471):n.407+7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 534,400 control chromosomes in the GnomAD database, including 91,601 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 0.54 ( 22495 hom., cov: 32)

Exomes 𝑓: 0.60 ( 69106 hom. )

Consequence

LINC00471
ENST00000313064.5 splice_region, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.283

Publications

27 publications found

Variant links:

Genes affected

LINC00471 (HGNC:28668): (long intergenic non-protein coding RNA 471)

LINC00471 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000313064.5, 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000313064.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LINC00471	NR_024079.1	n.364+7A>G	splice_region intron	N/A
LINC00471	NR_199860.1	n.402+7A>G	splice_region intron	N/A
LINC00471	NR_199861.1	n.402+7A>G	splice_region intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC00471	ENST00000313064.5	TSL:1	n.407+7A>G	splice_region intron	N/A
LINC00471	ENST00000750607.1		n.900A>G	non_coding_transcript_exon	Exon 1 of 1
LINC00471	ENST00000750608.1		n.381A>G	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.536

AC:

81368

AN:

151914

Hom.:

22469

Cov.:

show subpopulations

Gnomad AFR

AF:

0.409

Gnomad AMI

AF:

0.614

Gnomad AMR

AF:

0.604

Gnomad ASJ

AF:

0.716

Gnomad EAS

AF:

0.726

Gnomad SAS

AF:

0.693

Gnomad FIN

AF:

0.567

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.554

Gnomad OTH

AF:

0.579

GnomAD2 exomes

AF:

0.597

AC:

150093

AN:

251380

AF XY:

0.601

show subpopulations

Gnomad AFR exome

AF:

0.399

Gnomad AMR exome

AF:

0.664

Gnomad ASJ exome

AF:

0.721

Gnomad EAS exome

AF:

0.718

Gnomad FIN exome

AF:

0.568

Gnomad NFE exome

AF:

0.562

Gnomad OTH exome

AF:

0.607

GnomAD4 exome

AF:

0.597

AC:

228109

AN:

382368

Hom.:

69106

Cov.:

AF XY:

0.602

AC XY:

131126

AN XY:

217682

show subpopulations

African (AFR)

AF:

0.402

AC:

4227

AN:

10514

American (AMR)

AF:

0.667

AC:

24211

AN:

36300

Ashkenazi Jewish (ASJ)

AF:

0.717

AC:

8413

AN:

11740

East Asian (EAS)

AF:

0.720

AC:

9485

AN:

13172

South Asian (SAS)

AF:

0.659

AC:

43988

AN:

66752

European-Finnish (FIN)

AF:

0.569

AC:

18357

AN:

32264

Middle Eastern (MID)

AF:

0.641

AC:

1828

AN:

2854

European-Non Finnish (NFE)

AF:

0.561

AC:

107695

AN:

192048

Other (OTH)

AF:

0.592

AC:

9905

AN:

16724

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

5389

10778

16166

21555

26944

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

892

1784

2676

3568

4460

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.536

AC:

81428

AN:

152032

Hom.:

22495

Cov.:

AF XY:

0.541

AC XY:

40240

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.409

AC:

16972

AN:

41466

American (AMR)

AF:

0.605

AC:

9240

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.716

AC:

2483

AN:

3470

East Asian (EAS)

AF:

0.726

AC:

3757

AN:

5174

South Asian (SAS)

AF:

0.692

AC:

3338

AN:

4826

European-Finnish (FIN)

AF:

0.567

AC:

5988

AN:

10552

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.554

AC:

37674

AN:

67952

Other (OTH)

AF:

0.584

AC:

1233

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1942

3883

5825

7766

9708

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

712

1424

2136

2848

3560

<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:

0.560

Hom.:

69328

Bravo

AF:

0.533

Asia WGS

AF:

0.737

AC:

2558

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.1

(source)

DANN

Benign

0.72

PhyloP100

-0.28

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over