Variant rs1378506 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 0.548 in 151,950 control chromosomes in the GnomAD database, including 23,080 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 0.55 ( 23080 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.284

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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:

0.548

AC:

83185

AN:

151832

Hom.:

23071

Cov.:

show subpopulations

Gnomad AFR

AF:

0.480

Gnomad AMI

AF:

0.413

Gnomad AMR

AF:

0.586

Gnomad ASJ

AF:

0.556

Gnomad EAS

AF:

0.775

Gnomad SAS

AF:

0.646

Gnomad FIN

AF:

0.603

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.540

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

GnomAD4 genome

AF:

0.548

AC:

83234

AN:

151950

Hom.:

23080

Cov.:

AF XY:

0.557

AC XY:

41339

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.480

Gnomad4 AMR

AF:

0.585

Gnomad4 ASJ

AF:

0.556

Gnomad4 EAS

AF:

0.776

Gnomad4 SAS

AF:

0.645

Gnomad4 FIN

AF:

0.603

Gnomad4 NFE

AF:

0.550

Gnomad4 OTH

AF:

0.539

Alfa

AF:

0.552

Hom.:

38829

Bravo

AF:

0.540

Asia WGS

AF:

0.650

AC:

2256

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.25

DANN

Benign

0.67

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