Variant 10-83868459-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 0.403 in 151,642 control chromosomes in the GnomAD database, including 12,403 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 0.40 ( 12403 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.375

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 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:

0.403

AC:

61014

AN:

151522

Hom.:

12379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.384

Gnomad AMI

AF:

0.497

Gnomad AMR

AF:

0.438

Gnomad ASJ

AF:

0.439

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.313

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.425

Gnomad OTH

AF:

0.442

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

GnomAD4 genome

AF:

0.403

AC:

61088

AN:

151642

Hom.:

12403

Cov.:

AF XY:

0.400

AC XY:

29636

AN XY:

74112

show subpopulations

Gnomad4 AFR

AF:

0.384

Gnomad4 AMR

AF:

0.437

Gnomad4 ASJ

AF:

0.439

Gnomad4 EAS

AF:

0.332

Gnomad4 SAS

AF:

0.352

Gnomad4 FIN

AF:

0.313

Gnomad4 NFE

AF:

0.425

Gnomad4 OTH

AF:

0.440

Alfa

AF:

0.424

Hom.:

27228

Bravo

AF:

0.416

Asia WGS

AF:

0.323

AC:

1122

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.89

DANN

Benign

0.35

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