Variant rs1471233 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 0.537 in 152,630 control chromosomes in the GnomAD database, including 22,355 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 0.54 ( 22280 hom., cov: 32)

Exomes 𝑓: 0.47 ( 75 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.00

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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.599 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:

0.538

AC:

81652

AN:

151886

Hom.:

22245

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.535

Gnomad AMR

AF:

0.609

Gnomad ASJ

AF:

0.417

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.574

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.576

Gnomad OTH

AF:

0.538

GnomAD4 exome

AF:

0.471

AC:

295

AN:

626

Hom.:

AF XY:

0.484

AC XY:

155

AN XY:

320

show subpopulations

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.483

Gnomad4 NFE exome

AF:

0.667

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.538

AC:

81738

AN:

152004

Hom.:

22280

Cov.:

AF XY:

0.538

AC XY:

39935

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.609

Gnomad4 ASJ

AF:

0.417

Gnomad4 EAS

AF:

0.509

Gnomad4 SAS

AF:

0.459

Gnomad4 FIN

AF:

0.574

Gnomad4 NFE

AF:

0.576

Gnomad4 OTH

AF:

0.542

Alfa

AF:

0.564

Hom.:

4158

Bravo

AF:

0.541

Asia WGS

AF:

0.485

AC:

1687

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.069

DANN

Benign

0.61

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