Variant X-853959-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 0.311 in 151,480 control chromosomes in the GnomAD database, including 9,083 homozygotes. There are 23,148 hemizygotes in GnomAD. 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 0.31 ( 9083 hom., 23148 hem., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 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:

0.311

AC:

47148

AN:

151362

Hom.:

9071

Cov.:

AF XY:

0.313

AC XY:

23104

AN XY:

73810

show subpopulations

Gnomad AFR

AF:

0.535

Gnomad AMI

AF:

0.222

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.456

Gnomad SAS

AF:

0.344

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.213

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.248

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

GnomAD4 genome

AF:

0.311

AC:

47180

AN:

151480

Hom.:

9083

Cov.:

AF XY:

0.313

AC XY:

23148

AN XY:

73938

show subpopulations

Gnomad4 AFR

AF:

0.535

Gnomad4 AMR

AF:

0.252

Gnomad4 ASJ

AF:

0.132

Gnomad4 EAS

AF:

0.456

Gnomad4 SAS

AF:

0.341

Gnomad4 FIN

AF:

0.257

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.245

Bravo

AF:

0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.8

DANN

Benign

0.73

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