dbSNP rs4534897: LINC00910:n.834+1952T>C (chr17-43354440-A-G) – 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+1952T>C 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 152,088 control chromosomes in the GnomAD database, including 8,129 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 ( 8129 hom., cov: 32)

Consequence

LINC00910
ENST00000658096.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.98

Publications

11 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=-0.9).

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+1952T>C	intron_variant	Intron 5 of 6
LINC00910	ENST00000661340.1 link	n.709-5111T>C	intron_variant	Intron 4 of 4
LINC00910	ENST00000662750.1 link	n.709-12981T>C	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.320

AC:

48638

AN:

151970

Hom.:

8123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.238

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.369

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.405

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:

48668

AN:

152088

Hom.:

8129

Cov.:

AF XY:

0.326

AC XY:

24263

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.238

AC:

9879

AN:

41498

American (AMR)

AF:

0.332

AC:

5068

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.360

AC:

1250

AN:

3472

East Asian (EAS)

AF:

0.369

AC:

1906

AN:

5168

South Asian (SAS)

AF:

0.495

AC:

2383

AN:

4818

European-Finnish (FIN)

AF:

0.405

AC:

4277

AN:

10560

Middle Eastern (MID)

AF:

0.357

AC:

105

AN:

294

European-Non Finnish (NFE)

AF:

0.336

AC:

22826

AN:

67986

Other (OTH)

AF:

0.339

AC:

714

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1656

3312

4969

6625

8281

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:

0.338

Hom.:

5710

Bravo

AF:

0.306

Asia WGS

AF:

0.416

AC:

1446

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.1

(source)

DANN

Benign

0.38

PhyloP100

-2.0

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