Genetic Variant ENSG00000250333:n.56-4630G>A (chr4-57629942-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000507808.1(ENSG00000250333):n.56-4630G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 152,146 control chromosomes in the GnomAD database, including 455 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 0.048 ( 455 hom., cov: 33)

Consequence

ENSG00000250333
ENST00000507808.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.74

Publications

1 publications found

Variant links:

Genes affected

ENSG00000250333 (HGNC:):

ENSG00000250333 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 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
ENSG00000250333	ENST00000507808.1 link	n.56-4630G>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0478

AC:

7269

AN:

152028

Hom.:

449

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0564

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.0262

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.0664

Gnomad FIN

AF:

0.0425

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00747

Gnomad OTH

AF:

0.0527

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

GnomAD4 genome

AF:

0.0479

AC:

7290

AN:

152146

Hom.:

455

Cov.:

AF XY:

0.0533

AC XY:

3963

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.0566

AC:

2350

AN:

41516

American (AMR)

AF:

0.137

AC:

2091

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0262

AC:

AN:

3470

East Asian (EAS)

AF:

0.263

AC:

1361

AN:

5166

South Asian (SAS)

AF:

0.0660

AC:

318

AN:

4818

European-Finnish (FIN)

AF:

0.0425

AC:

450

AN:

10590

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00747

AC:

508

AN:

67996

Other (OTH)

AF:

0.0526

AC:

111

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

336

672

1007

1343

1679

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<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:

0.0261

Hom.:

108

Bravo

AF:

0.0563

Asia WGS

AF:

0.136

AC:

471

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.17

(source)

DANN

Benign

0.70

PhyloP100

-3.7

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