Variant chr5-135020110-A-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 0.385 in 151,922 control chromosomes in the GnomAD database, including 12,097 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 ( 12097 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

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=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.549 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:

0.385

AC:

58450

AN:

151804

Hom.:

12072

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.511

Gnomad AMR

AF:

0.494

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.552

Gnomad SAS

AF:

0.567

Gnomad FIN

AF:

0.382

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.378

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

GnomAD4 genome

AF:

0.385

AC:

58502

AN:

151922

Hom.:

12097

Cov.:

AF XY:

0.389

AC XY:

28854

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.496

Gnomad4 ASJ

AF:

0.352

Gnomad4 EAS

AF:

0.551

Gnomad4 SAS

AF:

0.567

Gnomad4 FIN

AF:

0.382

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.385

Alfa

AF:

0.397

Hom.:

1550

Bravo

AF:

0.383

Asia WGS

AF:

0.577

AC:

2006

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.70

DANN

Benign

0.64

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