Variant rs10486270 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 0.271 in 151,774 control chromosomes in the GnomAD database, including 6,124 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 0.27 ( 6124 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.257

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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 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:

0.271

AC:

41113

AN:

151656

Hom.:

6122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.177

Gnomad AMI

AF:

0.345

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.0855

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.279

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.329

Gnomad OTH

AF:

0.295

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

GnomAD4 genome

AF:

0.271

AC:

41141

AN:

151774

Hom.:

6124

Cov.:

AF XY:

0.266

AC XY:

19772

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.177

Gnomad4 AMR

AF:

0.318

Gnomad4 ASJ

AF:

0.349

Gnomad4 EAS

AF:

0.0859

Gnomad4 SAS

AF:

0.207

Gnomad4 FIN

AF:

0.279

Gnomad4 NFE

AF:

0.329

Gnomad4 OTH

AF:

0.296

Alfa

AF:

0.183

Hom.:

422

Bravo

AF:

0.271

Asia WGS

AF:

0.187

AC:

649

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.0

DANN

Benign

0.56

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