Genetic Variant ENSG00000248428:n.483-1019A>G (chr5-110972184-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 ENST00000507627.1(ENSG00000248428):n.483-1019A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,104 control chromosomes in the GnomAD database, including 8,118 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 0.25 ( 8118 hom., cov: 33)

Consequence

ENSG00000248428
ENST00000507627.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.228

Publications

2 publications found

Variant links:

Genes affected

ENSG00000248428 (HGNC:):

ENSG00000248428 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 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
ENSG00000248428	ENST00000507627.1 link	n.483-1019A>G		intron_variant	Intron 5 of 5	5
ENSG00000298655	ENST00000757131.1 link	n.115-734T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37274

AN:

151986

Hom.:

8083

Cov.:

show subpopulations

Gnomad AFR

AF:

0.580

Gnomad AMI

AF:

0.114

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.0886

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0831

Gnomad OTH

AF:

0.224

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

GnomAD4 genome

AF:

0.246

AC:

37377

AN:

152104

Hom.:

8118

Cov.:

AF XY:

0.245

AC XY:

18184

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.580

AC:

24072

AN:

41482

American (AMR)

AF:

0.212

AC:

3244

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0886

AC:

307

AN:

3466

East Asian (EAS)

AF:

0.276

AC:

1426

AN:

5174

South Asian (SAS)

AF:

0.198

AC:

955

AN:

4822

European-Finnish (FIN)

AF:

0.105

AC:

1115

AN:

10618

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0831

AC:

5646

AN:

67942

Other (OTH)

AF:

0.225

AC:

476

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1097

2194

3291

4388

5485

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<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:

0.125

Hom.:

1219

Bravo

AF:

0.267

Asia WGS

AF:

0.242

AC:

842

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.7

(source)

DANN

Benign

0.84

PhyloP100

-0.23

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