Variant rs1326384 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 0.432 in 152,110 control chromosomes in the GnomAD database, including 16,314 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 0.43 ( 16314 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0230

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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.654 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:

0.432

AC:

65703

AN:

151994

Hom.:

16308

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.468

Gnomad ASJ

AF:

0.494

Gnomad EAS

AF:

0.633

Gnomad SAS

AF:

0.672

Gnomad FIN

AF:

0.563

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.518

Gnomad OTH

AF:

0.458

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

GnomAD4 genome

AF:

0.432

AC:

65734

AN:

152110

Hom.:

16314

Cov.:

AF XY:

0.443

AC XY:

32929

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.182

Gnomad4 AMR

AF:

0.468

Gnomad4 ASJ

AF:

0.494

Gnomad4 EAS

AF:

0.633

Gnomad4 SAS

AF:

0.673

Gnomad4 FIN

AF:

0.563

Gnomad4 NFE

AF:

0.518

Gnomad4 OTH

AF:

0.463

Alfa

AF:

0.499

Hom.:

27055

Bravo

AF:

0.409

Asia WGS

AF:

0.630

AC:

2191

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.5

DANN

Benign

0.51

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