Genetic Variant ENST00000598131.1:n.257-18880G>T (chr19-20478202-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 ENST00000598131.1(ENSG00000269043):n.257-18880G>T variant causes a intron change. The variant allele was found at a frequency of 0.116 in 147,170 control chromosomes in the GnomAD database, including 1,788 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 0.12 ( 1788 hom., cov: 29)

Consequence

ENSG00000269043
ENST00000598131.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

No conservation score assigned

Publications

4 publications found

Variant links:

Genes affected

ENSG00000269043 (HGNC:):

ENSG00000269043 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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372316	XR_936408.3 link	n.145+5016G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000269043	ENST00000598131.1 link	n.257-18880G>T	intron_variant	Intron 2 of 3	3
ENSG00000269043	ENST00000653011.1 link	n.201+5016G>T	intron_variant	Intron 1 of 2
ENSG00000269043	ENST00000737268.1 link	n.53+5016G>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17089

AN:

147056

Hom.:

1792

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0835

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.000619

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.0980

Gnomad NFE

AF:

0.136

Gnomad OTH

AF:

0.109

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

GnomAD4 genome

AF:

0.116

AC:

17080

AN:

147170

Hom.:

1788

Cov.:

AF XY:

0.115

AC XY:

8267

AN XY:

71632

show subpopulations

African (AFR)

AF:

0.0834

AC:

3323

AN:

39832

American (AMR)

AF:

0.107

AC:

1568

AN:

14684

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

437

AN:

3340

East Asian (EAS)

AF:

0.000621

AC:

AN:

4832

South Asian (SAS)

AF:

0.117

AC:

495

AN:

4218

European-Finnish (FIN)

AF:

0.160

AC:

1643

AN:

10298

Middle Eastern (MID)

AF:

0.0876

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.136

AC:

9106

AN:

66838

Other (OTH)

AF:

0.106

AC:

213

AN:

2004

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

654

1308

1963

2617

3271

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.129

Hom.:

803

Asia WGS

AF:

0.0560

AC:

197

AN:

3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

3.0

(source)

DANN

Benign

0.78

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