dbSNP rs4825220: ENSG00000298798:n.252+220A>G (chrX-140132319-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000758029.1(ENSG00000298798):n.252+220A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 110,451 control chromosomes in the GnomAD database, including 7,238 homozygotes. There are 12,638 hemizygotes in GnomAD. 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 0.39 ( 7238 hom., 12638 hem., cov: 22)

Consequence

ENSG00000298798
ENST00000758029.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Publications

1 publications found

Variant links:

Genes affected

ENSG00000298798 (HGNC:):

ENSG00000298798 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000298798	ENST00000758029.1 link	n.252+220A>G	intron_variant	Intron 2 of 2
ENSG00000298798	ENST00000758030.1 link	n.154-16461A>G	intron_variant	Intron 1 of 1
ENSG00000298798	ENST00000758031.1 link	n.*11A>G	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.388

AC:

42858

AN:

110408

Hom.:

7237

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0994

Gnomad AMI

AF:

0.463

Gnomad AMR

AF:

0.455

Gnomad ASJ

AF:

0.458

Gnomad EAS

AF:

0.546

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.496

Gnomad MID

AF:

0.366

Gnomad NFE

AF:

0.513

Gnomad OTH

AF:

0.398

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

GnomAD4 genome

AF:

0.388

AC:

42851

AN:

110451

Hom.:

7238

Cov.:

AF XY:

0.386

AC XY:

12638

AN XY:

32703

show subpopulations

African (AFR)

AF:

0.0991

AC:

3037

AN:

30633

American (AMR)

AF:

0.455

AC:

4700

AN:

10328

Ashkenazi Jewish (ASJ)

AF:

0.458

AC:

1202

AN:

2627

East Asian (EAS)

AF:

0.545

AC:

1882

AN:

3451

South Asian (SAS)

AF:

0.439

AC:

1135

AN:

2583

European-Finnish (FIN)

AF:

0.496

AC:

2848

AN:

5740

Middle Eastern (MID)

AF:

0.365

AC:

AN:

211

European-Non Finnish (NFE)

AF:

0.513

AC:

27053

AN:

52707

Other (OTH)

AF:

0.404

AC:

609

AN:

1506

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

844

1688

2531

3375

4219

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

400

800

1200

1600

2000

<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:

0.455

Hom.:

15127

Bravo

AF:

0.375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.0

(source)

DANN

Benign

0.73

PhyloP100

0.24

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