Variant chr6-89315393-G-T 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 0.176 in 983,492 control chromosomes in the GnomAD database, including 16,493 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 0.15 ( 2023 hom., cov: 32)

Exomes 𝑓: 0.18 ( 14470 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.343

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=-0.23).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 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:

0.152

AC:

23037

AN:

152044

Hom.:

2024

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0661

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.259

Gnomad FIN

AF:

0.169

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.170

GnomAD4 exome

AF:

0.181

AC:

150543

AN:

831328

Hom.:

14470

AF XY:

0.184

AC XY:

76501

AN XY:

415074

show subpopulations

Gnomad4 AFR exome

AF:

0.0594

Gnomad4 AMR exome

AF:

0.192

Gnomad4 ASJ exome

AF:

0.235

Gnomad4 EAS exome

AF:

0.207

Gnomad4 SAS exome

AF:

0.268

Gnomad4 FIN exome

AF:

0.169

Gnomad4 NFE exome

AF:

0.176

Gnomad4 OTH exome

AF:

0.184

GnomAD4 genome

AF:

0.151

AC:

23043

AN:

152164

Hom.:

2023

Cov.:

AF XY:

0.156

AC XY:

11580

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.0660

Gnomad4 AMR

AF:

0.183

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.190

Gnomad4 SAS

AF:

0.258

Gnomad4 FIN

AF:

0.169

Gnomad4 NFE

AF:

0.176

Gnomad4 OTH

AF:

0.176

Alfa

AF:

0.175

Hom.:

4095

Bravo

AF:

0.146

Asia WGS

AF:

0.226

AC:

785

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.23

CADD

Benign

DANN

Benign

0.78

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