Variant 5-30984192-G-T 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 0.449 in 151,904 control chromosomes in the GnomAD database, including 15,536 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 0.45 ( 15536 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0800

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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 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:

0.449

AC:

68113

AN:

151784

Hom.:

15522

Cov.:

show subpopulations

Gnomad AFR

AF:

0.506

Gnomad AMI

AF:

0.454

Gnomad AMR

AF:

0.488

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.492

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.420

Gnomad OTH

AF:

0.438

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

GnomAD4 genome

AF:

0.449

AC:

68161

AN:

151904

Hom.:

15536

Cov.:

AF XY:

0.448

AC XY:

33255

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.505

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.358

Gnomad4 EAS

AF:

0.492

Gnomad4 SAS

AF:

0.372

Gnomad4 FIN

AF:

0.400

Gnomad4 NFE

AF:

0.420

Gnomad4 OTH

AF:

0.438

Alfa

AF:

0.414

Hom.:

20350

Bravo

AF:

0.463

Asia WGS

AF:

0.400

AC:

1392

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.92

DANN

Benign

0.41

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