Variant rs722345 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 0.305 in 151,848 control chromosomes in the GnomAD database, including 8,058 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 0.30 ( 8058 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.147

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=-0.66).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 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:

0.305

AC:

46319

AN:

151730

Hom.:

8062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.411

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.397

Gnomad EAS

AF:

0.0640

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.350

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.416

Gnomad OTH

AF:

0.312

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

GnomAD4 genome

AF:

0.305

AC:

46307

AN:

151848

Hom.:

8058

Cov.:

AF XY:

0.298

AC XY:

22078

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.160

Gnomad4 AMR

AF:

0.237

Gnomad4 ASJ

AF:

0.397

Gnomad4 EAS

AF:

0.0643

Gnomad4 SAS

AF:

0.261

Gnomad4 FIN

AF:

0.350

Gnomad4 NFE

AF:

0.416

Gnomad4 OTH

AF:

0.309

Alfa

AF:

0.353

Hom.:

3206

Bravo

AF:

0.290

Asia WGS

AF:

0.149

AC:

517

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

8.2

DANN

Benign

0.94

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