Genetic Variant LINC00970:n.131+1934A>G (chr1-169101212-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 ENST00000650631.1(LINC00970):n.131+1934A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,128 control chromosomes in the GnomAD database, including 2,214 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 0.16 ( 2214 hom., cov: 32)

Consequence

LINC00970
ENST00000650631.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.850

Publications

17 publications found

Variant links:

Genes affected

LINC00970 (HGNC:48730): (long intergenic non-protein coding RNA 970)

LINC00970 links:

LINC00970 (HGNC:):

LINC00970 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00970	ENST00000650631.1 link	n.131+1934A>G	intron_variant	Intron 1 of 8
LINC00970	ENST00000715524.1 link	n.131+1934A>G	intron_variant	Intron 1 of 9
LINC00970	ENST00000715525.1 link	n.132+1934A>G	intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23752

AN:

152010

Hom.:

2213

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.0504

Gnomad SAS

AF:

0.0628

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.162

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

GnomAD4 genome

AF:

0.156

AC:

23777

AN:

152128

Hom.:

2214

Cov.:

AF XY:

0.154

AC XY:

11468

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.260

AC:

10771

AN:

41440

American (AMR)

AF:

0.118

AC:

1808

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.201

AC:

697

AN:

3468

East Asian (EAS)

AF:

0.0503

AC:

260

AN:

5170

South Asian (SAS)

AF:

0.0633

AC:

305

AN:

4822

European-Finnish (FIN)

AF:

0.123

AC:

1301

AN:

10600

Middle Eastern (MID)

AF:

0.255

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8173

AN:

68018

Other (OTH)

AF:

0.160

AC:

338

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1006

2013

3019

4026

5032

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

240

480

720

960

1200

<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:

0.133

Hom.:

3223

Bravo

AF:

0.159

Asia WGS

AF:

0.0680

AC:

238

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.99

(source)

DANN

Benign

0.72

PhyloP100

-0.85

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