Genetic Variant ENSG00000283782:c.-168-24287T>C (chr5-132534997-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000638452.2(ENSG00000283782):c.-168-24287T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,008 control chromosomes in the GnomAD database, including 11,476 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 0.38 ( 11476 hom., cov: 31)

Consequence

ENSG00000283782
ENST00000638452.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0780

Publications

4 publications found

Variant links:

Genes affected

ENSG00000283782 (HGNC:):

ENSG00000283782 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283782	ENST00000638452.2 link	c.-168-24287T>C		intron_variant	Intron 3 of 26	5		ENSP00000492349.2		A0A1W2PQ90

Frequencies

GnomAD3 genomes

AF:

0.378

AC:

57382

AN:

151890

Hom.:

11462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.454

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.350

Gnomad ASJ

AF:

0.375

Gnomad EAS

AF:

0.692

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.414

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

GnomAD4 genome

AF:

0.378

AC:

57434

AN:

152008

Hom.:

11476

Cov.:

AF XY:

0.375

AC XY:

27844

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.454

AC:

18805

AN:

41446

American (AMR)

AF:

0.350

AC:

5333

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.375

AC:

1300

AN:

3470

East Asian (EAS)

AF:

0.692

AC:

3576

AN:

5170

South Asian (SAS)

AF:

0.349

AC:

1684

AN:

4820

European-Finnish (FIN)

AF:

0.276

AC:

2915

AN:

10562

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.330

AC:

22402

AN:

67962

Other (OTH)

AF:

0.416

AC:

880

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1782

3564

5346

7128

8910

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.355

Hom.:

29741

Bravo

AF:

0.394

Asia WGS

AF:

0.512

AC:

1780

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.4

(source)

DANN

Benign

0.73

PhyloP100

0.078

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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5-132534997-T-C

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