Genetic Variant LINC00910:n.834+100C>A (chr17-43356292-G-T) – 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+100C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,070 control chromosomes in the GnomAD database, including 5,016 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 0.25 ( 5016 hom., cov: 32)

Consequence

LINC00910
ENST00000658096.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.197

Publications

17 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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 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+100C>A	intron_variant	Intron 5 of 6
LINC00910	ENST00000661340.1 link	n.709-6963C>A	intron_variant	Intron 4 of 4
LINC00910	ENST00000662750.1 link	n.709-14833C>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37304

AN:

151952

Hom.:

5014

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.264

Gnomad EAS

AF:

0.369

Gnomad SAS

AF:

0.463

Gnomad FIN

AF:

0.309

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.260

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

GnomAD4 genome

AF:

0.245

AC:

37306

AN:

152070

Hom.:

5016

Cov.:

AF XY:

0.252

AC XY:

18747

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.156

AC:

6486

AN:

41498

American (AMR)

AF:

0.268

AC:

4101

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.264

AC:

914

AN:

3468

East Asian (EAS)

AF:

0.368

AC:

1899

AN:

5154

South Asian (SAS)

AF:

0.462

AC:

2227

AN:

4816

European-Finnish (FIN)

AF:

0.309

AC:

3260

AN:

10564

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.258

AC:

17567

AN:

67976

Other (OTH)

AF:

0.264

AC:

558

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1386

2772

4157

5543

6929

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.253

Hom.:

7734

Bravo

AF:

0.232

Asia WGS

AF:

0.388

AC:

1349

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.1

(source)

DANN

Benign

0.33

PhyloP100

0.20

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