Variant 1-105095799-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 0.594 in 151,942 control chromosomes in the GnomAD database, including 27,452 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 0.59 ( 27452 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.95

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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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:

0.595

AC:

90274

AN:

151822

Hom.:

27444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.468

Gnomad AMI

AF:

0.729

Gnomad AMR

AF:

0.632

Gnomad ASJ

AF:

0.631

Gnomad EAS

AF:

0.677

Gnomad SAS

AF:

0.576

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.651

Gnomad OTH

AF:

0.604

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

GnomAD4 genome

AF:

0.594

AC:

90322

AN:

151942

Hom.:

27452

Cov.:

AF XY:

0.595

AC XY:

44168

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.468

Gnomad4 AMR

AF:

0.633

Gnomad4 ASJ

AF:

0.631

Gnomad4 EAS

AF:

0.678

Gnomad4 SAS

AF:

0.576

Gnomad4 FIN

AF:

0.614

Gnomad4 NFE

AF:

0.651

Gnomad4 OTH

AF:

0.599

Alfa

AF:

0.634

Hom.:

15258

Bravo

AF:

0.594

Asia WGS

AF:

0.601

AC:

2085

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.0040

DANN

Benign

0.19

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