Variant rs1548882 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 0.605 in 151,154 control chromosomes in the GnomAD database, including 28,409 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 0.60 ( 28409 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.324

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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 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:

0.604

AC:

91303

AN:

151040

Hom.:

28378

Cov.:

show subpopulations

Gnomad AFR

AF:

0.760

Gnomad AMI

AF:

0.441

Gnomad AMR

AF:

0.599

Gnomad ASJ

AF:

0.546

Gnomad EAS

AF:

0.606

Gnomad SAS

AF:

0.634

Gnomad FIN

AF:

0.535

Gnomad MID

AF:

0.609

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.580

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

GnomAD4 genome

AF:

0.605

AC:

91392

AN:

151154

Hom.:

28409

Cov.:

AF XY:

0.607

AC XY:

44835

AN XY:

73842

show subpopulations

Gnomad4 AFR

AF:

0.761

Gnomad4 AMR

AF:

0.599

Gnomad4 ASJ

AF:

0.546

Gnomad4 EAS

AF:

0.608

Gnomad4 SAS

AF:

0.632

Gnomad4 FIN

AF:

0.535

Gnomad4 NFE

AF:

0.525

Gnomad4 OTH

AF:

0.578

Alfa

AF:

0.545

Hom.:

5600

Bravo

AF:

0.616

Asia WGS

AF:

0.604

AC:

2080

AN:

3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.0

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