dbSNP rs2831605: LINC01695:n.524-2731G>A (chr21-28172874-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000453420.5(LINC01695):n.524-2731G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 151,660 control chromosomes in the GnomAD database, including 1,222 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 0.12 ( 1222 hom., cov: 31)

Consequence

LINC01695
ENST00000453420.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.823

Publications

6 publications found

Variant links:

Genes affected

LINC01695 (HGNC:52483): (long intergenic non-protein coding RNA 1695)

LINC01695 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01695	NR_126012.1 link	n.524-2731G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01695	ENST00000453420.5 link	n.524-2731G>A		intron_variant	Intron 3 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18776

AN:

151546

Hom.:

1217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.157

Gnomad EAS

AF:

0.00620

Gnomad SAS

AF:

0.0547

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.159

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.131

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

GnomAD4 genome

AF:

0.124

AC:

18794

AN:

151660

Hom.:

1222

Cov.:

AF XY:

0.123

AC XY:

9125

AN XY:

74096

show subpopulations

African (AFR)

AF:

0.127

AC:

5254

AN:

41376

American (AMR)

AF:

0.112

AC:

1711

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

544

AN:

3462

East Asian (EAS)

AF:

0.00622

AC:

AN:

5148

South Asian (SAS)

AF:

0.0549

AC:

264

AN:

4806

European-Finnish (FIN)

AF:

0.155

AC:

1629

AN:

10490

Middle Eastern (MID)

AF:

0.161

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.133

AC:

9025

AN:

67846

Other (OTH)

AF:

0.130

AC:

274

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

842

1684

2526

3368

4210

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<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:

0.132

Hom.:

228

Bravo

AF:

0.122

Asia WGS

AF:

0.0450

AC:

160

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.0

(source)

DANN

Benign

0.82

PhyloP100

-0.82

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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