Variant rs1330320 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 0.4 in 151,908 control chromosomes in the GnomAD database, including 12,295 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 0.40 ( 12295 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.694

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 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:

0.400

AC:

60707

AN:

151790

Hom.:

12281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.409

Gnomad AMI

AF:

0.375

Gnomad AMR

AF:

0.420

Gnomad ASJ

AF:

0.370

Gnomad EAS

AF:

0.513

Gnomad SAS

AF:

0.318

Gnomad FIN

AF:

0.377

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.393

Gnomad OTH

AF:

0.393

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

GnomAD4 genome

AF:

0.400

AC:

60764

AN:

151908

Hom.:

12295

Cov.:

AF XY:

0.399

AC XY:

29637

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.409

Gnomad4 AMR

AF:

0.420

Gnomad4 ASJ

AF:

0.370

Gnomad4 EAS

AF:

0.513

Gnomad4 SAS

AF:

0.320

Gnomad4 FIN

AF:

0.377

Gnomad4 NFE

AF:

0.393

Gnomad4 OTH

AF:

0.391

Alfa

AF:

0.393

Hom.:

24186

Bravo

AF:

0.405

Asia WGS

AF:

0.403

AC:

1402

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.51

DANN

Benign

0.74

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