Variant rs1011170 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 0.313 in 152,040 control chromosomes in the GnomAD database, including 8,049 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 0.31 ( 8049 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.170

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=-0.33).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 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:

0.313

AC:

47517

AN:

151922

Hom.:

8042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.341

Gnomad ASJ

AF:

0.390

Gnomad EAS

AF:

0.734

Gnomad SAS

AF:

0.463

Gnomad FIN

AF:

0.325

Gnomad MID

AF:

0.376

Gnomad NFE

AF:

0.285

Gnomad OTH

AF:

0.334

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

GnomAD4 genome

AF:

0.313

AC:

47554

AN:

152040

Hom.:

8049

Cov.:

AF XY:

0.318

AC XY:

23655

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.267

Gnomad4 AMR

AF:

0.342

Gnomad4 ASJ

AF:

0.390

Gnomad4 EAS

AF:

0.733

Gnomad4 SAS

AF:

0.464

Gnomad4 FIN

AF:

0.325

Gnomad4 NFE

AF:

0.285

Gnomad4 OTH

AF:

0.339

Alfa

AF:

0.295

Hom.:

1144

Bravo

AF:

0.315

Asia WGS

AF:

0.516

AC:

1794

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Benign

0.85

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