Variant rs60515630 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.0078 in 1,242,332 control chromosomes in the GnomAD database, including 331 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.030 ( 203 hom., cov: 33)

Exomes 𝑓: 0.0047 ( 128 hom. )

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.538

Variant links:

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ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0302

AC:

4559

AN:

151016

Hom.:

203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0943

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0183

Gnomad ASJ

AF:

0.0278

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.0000971

Gnomad MID

AF:

0.0385

Gnomad NFE

AF:

0.00315

Gnomad OTH

AF:

0.0319

GnomAD4 exome

AF:

0.00469

AC:

5123

AN:

1091210

Hom.:

128

AF XY:

0.00452

AC XY:

2372

AN XY:

525240

show subpopulations

Gnomad4 AFR exome

AF:

0.0935

Gnomad4 AMR exome

AF:

0.0181

Gnomad4 ASJ exome

AF:

0.0325

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000527

Gnomad4 FIN exome

AF:

0.0000761

Gnomad4 NFE exome

AF:

0.00201

Gnomad4 OTH exome

AF:

0.0121

GnomAD4 genome

AF:

0.0302

AC:

4568

AN:

151122

Hom.:

203

Cov.:

AF XY:

0.0291

AC XY:

2147

AN XY:

73838

show subpopulations

Gnomad4 AFR

AF:

0.0943

Gnomad4 AMR

AF:

0.0182

Gnomad4 ASJ

AF:

0.0278

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.0000971

Gnomad4 NFE

AF:

0.00315

Gnomad4 OTH

AF:

0.0306

Alfa

AF:

0.0189

Hom.:

Bravo

AF:

0.0353

Asia WGS

AF:

0.00558

AC:

AN:

3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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