Variant 10-124456270-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 0.252 in 151,966 control chromosomes in the GnomAD database, including 5,773 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 0.25 ( 5773 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.198

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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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:

0.252

AC:

38220

AN:

151850

Hom.:

5779

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0889

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.395

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.278

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.242

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

GnomAD4 genome

AF:

0.252

AC:

38230

AN:

151966

Hom.:

5773

Cov.:

AF XY:

0.249

AC XY:

18523

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.0889

Gnomad4 AMR

AF:

0.281

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.396

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.278

Gnomad4 NFE

AF:

0.330

Gnomad4 OTH

AF:

0.242

Alfa

AF:

0.305

Hom.:

7307

Bravo

AF:

0.245

Asia WGS

AF:

0.234

AC:

813

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.1

DANN

Benign

0.58

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