Variant rs1006899 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 0.171 in 151,320 control chromosomes in the GnomAD database, including 2,286 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 0.17 ( 2286 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.11

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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 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:

0.171

AC:

25807

AN:

151202

Hom.:

2281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.0470

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.159

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.163

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

GnomAD4 genome

AF:

0.171

AC:

25835

AN:

151320

Hom.:

2286

Cov.:

AF XY:

0.170

AC XY:

12581

AN XY:

73900

show subpopulations

Gnomad4 AFR

AF:

0.209

Gnomad4 AMR

AF:

0.115

Gnomad4 ASJ

AF:

0.192

Gnomad4 EAS

AF:

0.0469

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.159

Gnomad4 NFE

AF:

0.166

Gnomad4 OTH

AF:

0.162

Alfa

AF:

0.163

Hom.:

3561

Bravo

AF:

0.165

Asia WGS

AF:

0.148

AC:

515

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.2

DANN

Benign

0.79

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