Variant chr9-5350548-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 0.478 in 152,050 control chromosomes in the GnomAD database, including 18,748 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 ( 18748 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.81

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=-1.08).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 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:

0.477

AC:

72502

AN:

151930

Hom.:

18711

Cov.:

show subpopulations

Gnomad AFR

AF:

0.673

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.466

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.434

Gnomad SAS

AF:

0.544

Gnomad FIN

AF:

0.348

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.380

Gnomad OTH

AF:

0.452

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

GnomAD4 genome

AF:

0.478

AC:

72612

AN:

152050

Hom.:

18748

Cov.:

AF XY:

0.476

AC XY:

35383

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.673

Gnomad4 AMR

AF:

0.467

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.434

Gnomad4 SAS

AF:

0.545

Gnomad4 FIN

AF:

0.348

Gnomad4 NFE

AF:

0.380

Gnomad4 OTH

AF:

0.458

Alfa

AF:

0.416

Hom.:

2307

Bravo

AF:

0.495

Asia WGS

AF:

0.512

AC:

1781

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

1.6

DANN

Benign

0.58

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