Genetic Variant ENSG00000226484:n.1404+2551G>A (chrX-36411364-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 ENST00000455438.2(ENSG00000226484):n.1404+2551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 110,418 control chromosomes in the GnomAD database, including 3,600 homozygotes. There are 5,057 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 0.17 ( 3600 hom., 5057 hem., cov: 22)

Consequence

ENSG00000226484
ENST00000455438.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.140

Publications

0 publications found

Variant links:

Genes affected

ENSG00000226484 (HGNC:):

ENSG00000226484 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928627	NR_110412.1 link	n.1404+2551G>A		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226484	ENST00000455438.2 link	n.1404+2551G>A		intron_variant	Intron 5 of 7	2

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

18794

AN:

110373

Hom.:

3599

Cov.:

show subpopulations

Gnomad AFR

AF:

0.563

Gnomad AMI

AF:

0.0278

Gnomad AMR

AF:

0.0691

Gnomad ASJ

AF:

0.00228

Gnomad EAS

AF:

0.00113

Gnomad SAS

AF:

0.0467

Gnomad FIN

AF:

0.00579

Gnomad MID

AF:

0.0603

Gnomad NFE

AF:

0.0140

Gnomad OTH

AF:

0.124

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

GnomAD4 genome

AF:

0.171

AC:

18839

AN:

110418

Hom.:

3600

Cov.:

AF XY:

0.154

AC XY:

5057

AN XY:

32760

show subpopulations

African (AFR)

AF:

0.563

AC:

17001

AN:

30189

American (AMR)

AF:

0.0689

AC:

716

AN:

10389

Ashkenazi Jewish (ASJ)

AF:

0.00228

AC:

AN:

2628

East Asian (EAS)

AF:

0.00113

AC:

AN:

3533

South Asian (SAS)

AF:

0.0472

AC:

123

AN:

2604

European-Finnish (FIN)

AF:

0.00579

AC:

AN:

5870

Middle Eastern (MID)

AF:

0.0613

AC:

AN:

212

European-Non Finnish (NFE)

AF:

0.0140

AC:

738

AN:

52802

Other (OTH)

AF:

0.123

AC:

185

AN:

1507

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

350

701

1051

1402

1752

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<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:

0.107

Hom.:

727

Bravo

AF:

0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.5

(source)

DANN

Benign

0.49

PhyloP100

0.14

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