dbSNP rs11651341: LINC00910:n.834+5699A>G (chr17-43350693-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 ENST00000658096.1(LINC00910):n.834+5699A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,032 control chromosomes in the GnomAD database, including 8,103 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 0.32 ( 8103 hom., cov: 32)

Consequence

LINC00910
ENST00000658096.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32

Publications

14 publications found

Variant links:

Genes affected

LINC00910 (HGNC:44361): (long intergenic non-protein coding RNA 910)

LINC00910 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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00910	ENST00000658096.1 link	n.834+5699A>G	intron_variant	Intron 5 of 6
LINC00910	ENST00000661340.1 link	n.709-1364A>G	intron_variant	Intron 4 of 4
LINC00910	ENST00000662750.1 link	n.709-9234A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.320

AC:

48556

AN:

151914

Hom.:

8097

Cov.:

show subpopulations

Gnomad AFR

AF:

0.236

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.370

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.335

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

GnomAD4 genome

AF:

0.320

AC:

48587

AN:

152032

Hom.:

8103

Cov.:

AF XY:

0.326

AC XY:

24234

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.236

AC:

9794

AN:

41466

American (AMR)

AF:

0.332

AC:

5067

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.360

AC:

1249

AN:

3470

East Asian (EAS)

AF:

0.370

AC:

1906

AN:

5158

South Asian (SAS)

AF:

0.495

AC:

2386

AN:

4824

European-Finnish (FIN)

AF:

0.406

AC:

4292

AN:

10572

Middle Eastern (MID)

AF:

0.357

AC:

105

AN:

294

European-Non Finnish (NFE)

AF:

0.336

AC:

22814

AN:

67954

Other (OTH)

AF:

0.339

AC:

714

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1672

3345

5017

6690

8362

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.325

Hom.:

15738

Bravo

AF:

0.305

Asia WGS

AF:

0.416

AC:

1447

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.0

(source)

DANN

Benign

0.45

PhyloP100

-1.3

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