Genetic Variant ENSG00000298132:n.127+1000G>T (chr20-47796832-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 ENST00000753201.1(ENSG00000298132):n.127+1000G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,250 control chromosomes in the GnomAD database, including 1,033 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 0.11 ( 1033 hom., cov: 33)

Consequence

ENSG00000298132
ENST00000753201.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.201

Publications

16 publications found

Variant links:

Genes affected

ENSG00000298132 (HGNC:):

ENSG00000298132 links:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985401	XR_001754648.3 link	n.319-1625G>T		intron_variant	Intron 1 of 1
LOC124904921	XR_007067619.1 link	n.189+112C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298132	ENST00000753201.1 link	n.127+1000G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

16972

AN:

152132

Hom.:

1033

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.0990

Gnomad ASJ

AF:

0.0528

Gnomad EAS

AF:

0.0204

Gnomad SAS

AF:

0.0631

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.0922

Gnomad OTH

AF:

0.109

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

GnomAD4 genome

AF:

0.112

AC:

16985

AN:

152250

Hom.:

1033

Cov.:

AF XY:

0.111

AC XY:

8252

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.168

AC:

6973

AN:

41526

American (AMR)

AF:

0.0988

AC:

1512

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0528

AC:

183

AN:

3468

East Asian (EAS)

AF:

0.0204

AC:

106

AN:

5186

South Asian (SAS)

AF:

0.0629

AC:

304

AN:

4832

European-Finnish (FIN)

AF:

0.118

AC:

1248

AN:

10606

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0922

AC:

6271

AN:

68016

Other (OTH)

AF:

0.107

AC:

226

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

795

1590

2385

3180

3975

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.0914

Hom.:

2073

Bravo

AF:

0.112

Asia WGS

AF:

0.0440

AC:

154

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.4

(source)

DANN

Benign

0.84

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