Variant rs13330176 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.241 in 152,118 control chromosomes in the GnomAD database, including 4,878 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 0.24 ( 4878 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.375

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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:

0.242

AC:

36711

AN:

151996

Hom.:

4874

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.443

Gnomad AMR

AF:

0.381

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.461

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.244

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.241

AC:

36718

AN:

152114

Hom.:

4878

Cov.:

AF XY:

0.242

AC XY:

18014

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.382

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.460

Gnomad4 SAS

AF:

0.237

Gnomad4 FIN

AF:

0.167

Gnomad4 NFE

AF:

0.229

Gnomad4 OTH

AF:

0.242

Alfa

AF:

0.123

Hom.:

181

Bravo

AF:

0.264

Asia WGS

AF:

0.300

AC:

1042

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.6

DANN

Benign

0.61

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