Variant rs71365421 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 0.211 in 151,438 control chromosomes in the GnomAD database, including 3,617 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 0.21 ( 3617 hom., cov: 29)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.936

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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:

0.211

AC:

31859

AN:

151320

Hom.:

3617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.319

Gnomad ASJ

AF:

0.284

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.223

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

GnomAD4 genome

AF:

0.211

AC:

31879

AN:

151438

Hom.:

3617

Cov.:

AF XY:

0.215

AC XY:

15914

AN XY:

73956

show subpopulations

Gnomad4 AFR

AF:

0.151

Gnomad4 AMR

AF:

0.318

Gnomad4 ASJ

AF:

0.284

Gnomad4 EAS

AF:

0.356

Gnomad4 SAS

AF:

0.287

Gnomad4 FIN

AF:

0.214

Gnomad4 NFE

AF:

0.203

Gnomad4 OTH

AF:

0.222

Alfa

AF:

0.0923

Hom.:

122

Bravo

AF:

0.216

Asia WGS

AF:

0.315

AC:

1092

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

0.91

DANN

Benign

0.62

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