dbSNP rs10494620: LINC01035:n.239+34003C>A (chr1-188939929-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000445072.1(LINC01035):n.239+34003C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 151,888 control chromosomes in the GnomAD database, including 77 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 0.022 ( 77 hom., cov: 32)

Consequence

LINC01035
ENST00000445072.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.805

Publications

1 publications found

Variant links:

Genes affected

LINC01035 (HGNC:49022): (long intergenic non-protein coding RNA 1035)

LINC01035 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 (EAS) allele frequency at 95% confidence interval = 0.0519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01035	NR_174955.1 link	n.255+34003C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01035	ENST00000445072.1 link	n.239+34003C>A		intron_variant	Intron 1 of 1	3
LINC01035	ENST00000658142.1 link	n.157+34003C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0219

AC:

3320

AN:

151770

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0512

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00890

Gnomad ASJ

AF:

0.00808

Gnomad EAS

AF:

0.0573

Gnomad SAS

AF:

0.0535

Gnomad FIN

AF:

0.00236

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00616

Gnomad OTH

AF:

0.0182

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

GnomAD4 genome

AF:

0.0219

AC:

3329

AN:

151888

Hom.:

Cov.:

AF XY:

0.0217

AC XY:

1614

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.0512

AC:

2123

AN:

41476

American (AMR)

AF:

0.00888

AC:

135

AN:

15196

Ashkenazi Jewish (ASJ)

AF:

0.00808

AC:

AN:

3466

East Asian (EAS)

AF:

0.0573

AC:

295

AN:

5152

South Asian (SAS)

AF:

0.0538

AC:

259

AN:

4818

European-Finnish (FIN)

AF:

0.00236

AC:

AN:

10604

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00616

AC:

418

AN:

67864

Other (OTH)

AF:

0.0204

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

165

331

496

662

827

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

152

190

<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:

0.00708

Hom.:

Bravo

AF:

0.0224

Asia WGS

AF:

0.0820

AC:

282

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.038

(source)

DANN

Benign

0.68

PhyloP100

-0.81

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