Variant rs41307258 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5BP4BA1

The variant allele was found at a frequency of 0.052 in 111,499 control chromosomes in the GnomAD database, including 301 homozygotes. There are 1,900 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely pathogenic (no stars).

Frequency

Genomes: 𝑓 0.052 ( 301 hom., 1899 hem., cov: 23)

Exomes 𝑓: 0.14 ( 0 hom. 1 hem. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.939

Variant links:

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ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

PP5

Variant X-80014614-T-A is Pathogenic according to our data. Variant chrX-80014614-T-A is described in Lovd as [Likely_pathogenic].

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8). . Strength limited to SUPPORTING due to the PP5.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0520

AC:

5793

AN:

111434

Hom.:

300

Cov.:

AF XY:

0.0565

AC XY:

1899

AN XY:

33640

show subpopulations

Gnomad AFR

AF:

0.0275

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.0615

Gnomad ASJ

AF:

0.0212

Gnomad EAS

AF:

0.431

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.0961

Gnomad MID

AF:

0.0252

Gnomad NFE

AF:

0.0331

Gnomad OTH

AF:

0.0662

GnomAD4 exome

AF:

0.143

AC:

AN:

Hom.:

AF XY:

0.200

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.200

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0520

AC:

5800

AN:

111492

Hom.:

301

Cov.:

AF XY:

0.0563

AC XY:

1899

AN XY:

33708

show subpopulations

Gnomad4 AFR

AF:

0.0277

Gnomad4 AMR

AF:

0.0617

Gnomad4 ASJ

AF:

0.0212

Gnomad4 EAS

AF:

0.430

Gnomad4 SAS

AF:

0.106

Gnomad4 FIN

AF:

0.0961

Gnomad4 NFE

AF:

0.0331

Gnomad4 OTH

AF:

0.0674

Alfa

AF:

0.0404

Hom.:

208

Bravo

AF:

0.0551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.79

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over