Variant chr4-13097258-C-T 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 0.879 in 152,220 control chromosomes in the GnomAD database, including 58,903 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 0.88 ( 58903 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.69

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=-1.05).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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:

0.879

AC:

133736

AN:

152102

Hom.:

58859

Cov.:

show subpopulations

Gnomad AFR

AF:

0.894

Gnomad AMI

AF:

0.852

Gnomad AMR

AF:

0.907

Gnomad ASJ

AF:

0.847

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.928

Gnomad FIN

AF:

0.816

Gnomad MID

AF:

0.959

Gnomad NFE

AF:

0.863

Gnomad OTH

AF:

0.883

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

GnomAD4 genome

AF:

0.879

AC:

133838

AN:

152220

Hom.:

58903

Cov.:

AF XY:

0.879

AC XY:

65415

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.894

Gnomad4 AMR

AF:

0.908

Gnomad4 ASJ

AF:

0.847

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.928

Gnomad4 FIN

AF:

0.816

Gnomad4 NFE

AF:

0.863

Gnomad4 OTH

AF:

0.884

Alfa

AF:

0.872

Hom.:

68429

Bravo

AF:

0.887

Asia WGS

AF:

0.968

AC:

3364

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.14

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