Variant 5-99279461-C-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 0.305 in 151,942 control chromosomes in the GnomAD database, including 7,731 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 0.30 ( 7731 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.279

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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 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:

0.305

AC:

46306

AN:

151824

Hom.:

7722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.452

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.279

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.285

Gnomad FIN

AF:

0.282

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.247

Gnomad OTH

AF:

0.289

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

GnomAD4 genome

AF:

0.305

AC:

46337

AN:

151942

Hom.:

7731

Cov.:

AF XY:

0.302

AC XY:

22463

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.452

Gnomad4 AMR

AF:

0.233

Gnomad4 ASJ

AF:

0.279

Gnomad4 EAS

AF:

0.198

Gnomad4 SAS

AF:

0.285

Gnomad4 FIN

AF:

0.282

Gnomad4 NFE

AF:

0.247

Gnomad4 OTH

AF:

0.290

Alfa

AF:

0.276

Hom.:

1041

Bravo

AF:

0.309

Asia WGS

AF:

0.263

AC:

914

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.3

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