dbSNP rs10127000: LINC01278:n.255-5416C>A (chrX-63405319-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 ENST00000608788.7(LINC01278):n.255-5416C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 111,501 control chromosomes in the GnomAD database, including 4,069 homozygotes. There are 5,929 hemizygotes in GnomAD. 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 0.19 ( 4069 hom., 5929 hem., cov: 23)

Consequence

LINC01278
ENST00000608788.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640

Publications

2 publications found

Variant links:

Genes affected

LINC01278 (HGNC:28090): (long intergenic non-protein coding RNA 1278)

LINC01278 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01278	ENST00000608788.7 link	n.255-5416C>A	intron_variant	Intron 1 of 1	5
LINC01278	ENST00000610088.6 link	n.369-5416C>A	intron_variant	Intron 2 of 6	4
LINC01278	ENST00000610234.5 link	n.350-5416C>A	intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

21228

AN:

111449

Hom.:

4070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.597

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0872

Gnomad ASJ

AF:

0.0424

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0596

Gnomad FIN

AF:

0.0103

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0283

Gnomad OTH

AF:

0.170

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

GnomAD4 genome

AF:

0.191

AC:

21247

AN:

111501

Hom.:

4069

Cov.:

AF XY:

0.176

AC XY:

5929

AN XY:

33741

show subpopulations

African (AFR)

AF:

0.597

AC:

18214

AN:

30518

American (AMR)

AF:

0.0871

AC:

921

AN:

10572

Ashkenazi Jewish (ASJ)

AF:

0.0424

AC:

112

AN:

2640

East Asian (EAS)

AF:

0.00

AC:

AN:

3561

South Asian (SAS)

AF:

0.0602

AC:

161

AN:

2674

European-Finnish (FIN)

AF:

0.0103

AC:

AN:

6019

Middle Eastern (MID)

AF:

0.0876

AC:

AN:

217

European-Non Finnish (NFE)

AF:

0.0283

AC:

1502

AN:

53095

Other (OTH)

AF:

0.168

AC:

256

AN:

1524

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

369

738

1107

1476

1845

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<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:

0.0813

Hom.:

2321

Bravo

AF:

0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.4

(source)

DANN

Benign

0.36

PhyloP100

0.064

Mutation Taster

=100/0

polymorphism (auto)

(source)

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