Variant 4-122456825-A-C 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 0.256 in 166,840 control chromosomes in the GnomAD database, including 6,559 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 0.25 ( 5685 hom., cov: 32)

Exomes 𝑓: 0.33 ( 874 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

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=-0.49).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 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:

0.248

AC:

37699

AN:

151794

Hom.:

5671

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0736

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.298

Gnomad ASJ

AF:

0.430

Gnomad EAS

AF:

0.339

Gnomad SAS

AF:

0.504

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.299

Gnomad OTH

AF:

0.297

GnomAD4 exome

AF:

0.328

AC:

4903

AN:

14926

Hom.:

874

AF XY:

0.331

AC XY:

2429

AN XY:

7336

show subpopulations

Gnomad4 AFR exome

AF:

0.0876

Gnomad4 AMR exome

AF:

0.318

Gnomad4 ASJ exome

AF:

0.452

Gnomad4 EAS exome

AF:

0.375

Gnomad4 SAS exome

AF:

0.515

Gnomad4 FIN exome

AF:

0.343

Gnomad4 NFE exome

AF:

0.317

Gnomad4 OTH exome

AF:

0.330

GnomAD4 genome

AF:

0.248

AC:

37733

AN:

151914

Hom.:

5685

Cov.:

AF XY:

0.254

AC XY:

18877

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.0737

Gnomad4 AMR

AF:

0.299

Gnomad4 ASJ

AF:

0.430

Gnomad4 EAS

AF:

0.339

Gnomad4 SAS

AF:

0.506

Gnomad4 FIN

AF:

0.292

Gnomad4 NFE

AF:

0.299

Gnomad4 OTH

AF:

0.302

Alfa

AF:

0.286

Hom.:

3236

Bravo

AF:

0.237

Asia WGS

AF:

0.422

AC:

1467

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.67

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