Variant chr8-36988591-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 0.259 in 152,114 control chromosomes in the GnomAD database, including 5,944 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 0.26 ( 5944 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.743

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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 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:

0.259

AC:

39377

AN:

151996

Hom.:

5941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.406

Gnomad AMI

AF:

0.300

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.284

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.259

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

GnomAD4 genome

AF:

0.259

AC:

39397

AN:

152114

Hom.:

5944

Cov.:

AF XY:

0.259

AC XY:

19268

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.405

Gnomad4 AMR

AF:

0.232

Gnomad4 ASJ

AF:

0.284

Gnomad4 EAS

AF:

0.332

Gnomad4 SAS

AF:

0.306

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.184

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.205

Hom.:

4353

Bravo

AF:

0.267

Asia WGS

AF:

0.260

AC:

900

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.3

DANN

Benign

0.71

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