Variant 10-20349956-G-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 0.629 in 151,988 control chromosomes in the GnomAD database, including 30,813 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 0.63 ( 30807 hom., cov: 31)

Exomes 𝑓: 0.51 ( 6 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.223

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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 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:

0.629

AC:

95522

AN:

151802

Hom.:

30752

Cov.:

show subpopulations

Gnomad AFR

AF:

0.742

Gnomad AMI

AF:

0.657

Gnomad AMR

AF:

0.666

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.798

Gnomad SAS

AF:

0.592

Gnomad FIN

AF:

0.641

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.548

Gnomad OTH

AF:

0.590

GnomAD4 exome

AF:

0.515

AC:

AN:

Hom.:

AF XY:

0.550

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 EAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.522

Gnomad4 NFE exome

AF:

0.444

GnomAD4 genome

AF:

0.630

AC:

95638

AN:

151920

Hom.:

30807

Cov.:

AF XY:

0.632

AC XY:

46924

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.743

Gnomad4 AMR

AF:

0.666

Gnomad4 ASJ

AF:

0.500

Gnomad4 EAS

AF:

0.798

Gnomad4 SAS

AF:

0.592

Gnomad4 FIN

AF:

0.641

Gnomad4 NFE

AF:

0.548

Gnomad4 OTH

AF:

0.592

Alfa

AF:

0.558

Hom.:

40187

Bravo

AF:

0.638

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

Cadd

Benign

0.78

Dann

Benign

0.49

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