Variant rs378108 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.419 in 152,154 control chromosomes in the GnomAD database, including 14,660 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 0.42 ( 14660 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.561

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.25).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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:

0.420

AC:

63800

AN:

152036

Hom.:

14664

Cov.:

show subpopulations

Gnomad AFR

AF:

0.241

Gnomad AMI

AF:

0.374

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.424

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.442

Gnomad FIN

AF:

0.607

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.490

Gnomad OTH

AF:

0.414

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

GnomAD4 genome

AF:

0.419

AC:

63807

AN:

152154

Hom.:

14660

Cov.:

AF XY:

0.425

AC XY:

31631

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.241

Gnomad4 AMR

AF:

0.443

Gnomad4 ASJ

AF:

0.424

Gnomad4 EAS

AF:

0.462

Gnomad4 SAS

AF:

0.442

Gnomad4 FIN

AF:

0.607

Gnomad4 NFE

AF:

0.490

Gnomad4 OTH

AF:

0.411

Alfa

AF:

0.471

Hom.:

34970

Bravo

AF:

0.398

Asia WGS

AF:

0.433

AC:

1506

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.25

CADD

Benign

DANN

Benign

0.92

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