dbSNP rs1889055: :null (chr9-29539921-A-G) – ACMG Classification: Benign (-12 pts)

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 0.393 in 151,494 control chromosomes in the GnomAD database, including 12,255 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 0.39 ( 12255 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.453

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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59446

AN:

151376

Hom.:

12258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.430

Gnomad ASJ

AF:

0.453

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.506

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.411

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

GnomAD4 genome

AF:

0.393

AC:

59468

AN:

151494

Hom.:

12255

Cov.:

AF XY:

0.394

AC XY:

29174

AN XY:

74016

show subpopulations

Gnomad4 AFR

AF:

0.277

Gnomad4 AMR

AF:

0.431

Gnomad4 ASJ

AF:

0.453

Gnomad4 EAS

AF:

0.192

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.506

Gnomad4 NFE

AF:

0.454

Gnomad4 OTH

AF:

0.408

Alfa

AF:

0.439

Hom.:

30935

Bravo

AF:

0.384

Asia WGS

AF:

0.318

AC:

1105

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

7.4

DANN

Benign

0.47

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