Variant rs17318596 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP3BP6BA1

The variant allele was found at a frequency of 0.374 in 518,682 control chromosomes in the GnomAD database, including 38,178 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.33 ( 9188 hom., cov: 32)

Exomes 𝑓: 0.39 ( 28990 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.48

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

PP3

BayesDel_noAF computational evidence supports a deleterious effect, 0.15

BP6

Variant 19-41431190-G-A is Benign according to our data. Variant chr19-41431190-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50488

AN:

151862

Hom.:

9174

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.201

Gnomad AMR

AF:

0.422

Gnomad ASJ

AF:

0.371

Gnomad EAS

AF:

0.561

Gnomad SAS

AF:

0.403

Gnomad FIN

AF:

0.330

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.347

GnomAD3 exomes

AF:

0.398

AC:

91165

AN:

229234

Hom.:

19084

AF XY:

0.396

AC XY:

50181

AN XY:

126712

show subpopulations

Gnomad AFR exome

AF:

0.191

Gnomad AMR exome

AF:

0.507

Gnomad ASJ exome

AF:

0.374

Gnomad EAS exome

AF:

0.565

Gnomad SAS exome

AF:

0.402

Gnomad FIN exome

AF:

0.341

Gnomad NFE exome

AF:

0.370

Gnomad OTH exome

AF:

0.377

GnomAD4 exome

AF:

0.391

AC:

143302

AN:

366702

Hom.:

28990

Cov.:

AF XY:

0.392

AC XY:

82463

AN XY:

210264

show subpopulations

Gnomad4 AFR exome

AF:

0.196

Gnomad4 AMR exome

AF:

0.506

Gnomad4 ASJ exome

AF:

0.374

Gnomad4 EAS exome

AF:

0.559

Gnomad4 SAS exome

AF:

0.409

Gnomad4 FIN exome

AF:

0.340

Gnomad4 NFE exome

AF:

0.370

Gnomad4 OTH exome

AF:

0.369

GnomAD4 genome

AF:

0.333

AC:

50537

AN:

151980

Hom.:

9188

Cov.:

AF XY:

0.336

AC XY:

24959

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.197

Gnomad4 AMR

AF:

0.423

Gnomad4 ASJ

AF:

0.371

Gnomad4 EAS

AF:

0.560

Gnomad4 SAS

AF:

0.404

Gnomad4 FIN

AF:

0.330

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.350

Alfa

AF:

0.372

Hom.:

19415

Bravo

AF:

0.334

Asia WGS

AF:

0.465

AC:

1619

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Pathogenic

0.15

CADD

Benign

0.045

DANN

Benign

0.90

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