Variant 10-60776199-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 0.333 in 151,546 control chromosomes in the GnomAD database, including 8,803 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 0.33 ( 8803 hom., cov: 29)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 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:

0.333

AC:

50478

AN:

151426

Hom.:

8807

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.391

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.617

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.346

Gnomad MID

AF:

0.346

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.338

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

GnomAD4 genome

AF:

0.333

AC:

50500

AN:

151546

Hom.:

8803

Cov.:

AF XY:

0.334

AC XY:

24703

AN XY:

74032

show subpopulations

Gnomad4 AFR

AF:

0.257

Gnomad4 AMR

AF:

0.392

Gnomad4 ASJ

AF:

0.254

Gnomad4 EAS

AF:

0.618

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.346

Gnomad4 NFE

AF:

0.347

Gnomad4 OTH

AF:

0.336

Alfa

AF:

0.350

Hom.:

15530

Bravo

AF:

0.339

Asia WGS

AF:

0.453

AC:

1578

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.57

DANN

Benign

0.44

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