dbSNP rs644695: LINC00578:n.147+131799A>G (chr3-177573909-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 ENST00000439009.1(LINC00578):n.147+131799A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,262 control chromosomes in the GnomAD database, including 942 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 0.10 ( 942 hom., cov: 32)

Consequence

LINC00578
ENST00000439009.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0430

Publications

8 publications found

Variant links:

Genes affected

LINC00578 (HGNC:43807): (long intergenic non-protein coding RNA 578)

LINC00578 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00578	NR_047568.1 link	n.289+34416A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00578	ENST00000439009.1 link	n.147+131799A>G	intron_variant	Intron 1 of 1	4
LINC00578	ENST00000442937.6 link	n.289+34416A>G	intron_variant	Intron 2 of 3	3
LINC00578	ENST00000656037.1 link	n.185-55508A>G	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15455

AN:

152144

Hom.:

943

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0267

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.0313

Gnomad SAS

AF:

0.0957

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.138

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

GnomAD4 genome

AF:

0.101

AC:

15449

AN:

152262

Hom.:

942

Cov.:

AF XY:

0.0997

AC XY:

7423

AN XY:

74448

show subpopulations

African (AFR)

AF:

0.0266

AC:

1107

AN:

41568

American (AMR)

AF:

0.108

AC:

1660

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

512

AN:

3470

East Asian (EAS)

AF:

0.0313

AC:

162

AN:

5170

South Asian (SAS)

AF:

0.0966

AC:

466

AN:

4826

European-Finnish (FIN)

AF:

0.102

AC:

1078

AN:

10612

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.147

AC:

9991

AN:

67994

Other (OTH)

AF:

0.136

AC:

287

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

732

1464

2197

2929

3661

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<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:

0.131

Hom.:

4485

Bravo

AF:

0.0994

Asia WGS

AF:

0.0620

AC:

216

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.9

(source)

DANN

Benign

0.73

PhyloP100

-0.043

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