Genetic Variant LINC00701:n.47-816T>A (chr10-2307125-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000418295.1(LINC00701):n.47-816T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0414 in 152,272 control chromosomes in the GnomAD database, including 229 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 0.041 ( 229 hom., cov: 33)

Consequence

LINC00701
ENST00000418295.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.21

Publications

0 publications found

Variant links:

Genes affected

LINC00701 (HGNC:44674): (long intergenic non-protein coding RNA 701)

LINC00701 links:

Genome browser will be placed here

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=-0.77).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00701	NR_038884.1 link	n.46-816T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00701	ENST00000418295.1 link	n.47-816T>A	intron_variant	Intron 1 of 2	1
LINC00701	ENST00000721387.1 link	n.57-816T>A	intron_variant	Intron 1 of 5
LINC00701	ENST00000721388.1 link	n.47-816T>A	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.0413

AC:

6286

AN:

152154

Hom.:

225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0739

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0824

Gnomad ASJ

AF:

0.0176

Gnomad EAS

AF:

0.0850

Gnomad SAS

AF:

0.0172

Gnomad FIN

AF:

0.00612

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0177

Gnomad OTH

AF:

0.0450

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

GnomAD4 genome

AF:

0.0414

AC:

6308

AN:

152272

Hom.:

229

Cov.:

AF XY:

0.0410

AC XY:

3053

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.0740

AC:

3074

AN:

41546

American (AMR)

AF:

0.0829

AC:

1268

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0176

AC:

AN:

3472

East Asian (EAS)

AF:

0.0848

AC:

439

AN:

5176

South Asian (SAS)

AF:

0.0174

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00612

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0177

AC:

1205

AN:

68010

Other (OTH)

AF:

0.0460

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

298

596

894

1192

1490

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

210

280

350

<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:

0.00971

Hom.:

Bravo

AF:

0.0483

Asia WGS

AF:

0.0680

AC:

235

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

2.2

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