Variant rs4978076 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 0.484 in 152,024 control chromosomes in the GnomAD database, including 18,122 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 0.48 ( 18122 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 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:

0.484

AC:

73450

AN:

151906

Hom.:

18092

Cov.:

show subpopulations

Gnomad AFR

AF:

0.503

Gnomad AMI

AF:

0.532

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.464

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.560

Gnomad FIN

AF:

0.482

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.506

Gnomad OTH

AF:

0.451

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

GnomAD4 genome

AF:

0.484

AC:

73533

AN:

152024

Hom.:

18122

Cov.:

AF XY:

0.480

AC XY:

35664

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.504

Gnomad4 AMR

AF:

0.431

Gnomad4 ASJ

AF:

0.464

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.561

Gnomad4 FIN

AF:

0.482

Gnomad4 NFE

AF:

0.506

Gnomad4 OTH

AF:

0.447

Alfa

AF:

0.504

Hom.:

10410

Bravo

AF:

0.474

Asia WGS

AF:

0.395

AC:

1376

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

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