Variant chr1-115875282-T-A 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 0.232 in 152,142 control chromosomes in the GnomAD database, including 5,027 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 0.23 ( 5027 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.446

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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:

0.232

AC:

35333

AN:

152024

Hom.:

5024

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0614

Gnomad AMI

AF:

0.349

Gnomad AMR

AF:

0.346

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.312

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.280

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

GnomAD4 genome

AF:

0.232

AC:

35340

AN:

152142

Hom.:

5027

Cov.:

AF XY:

0.237

AC XY:

17628

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.0613

Gnomad4 AMR

AF:

0.345

Gnomad4 ASJ

AF:

0.324

Gnomad4 EAS

AF:

0.418

Gnomad4 SAS

AF:

0.312

Gnomad4 FIN

AF:

0.271

Gnomad4 NFE

AF:

0.277

Gnomad4 OTH

AF:

0.283

Alfa

AF:

0.255

Hom.:

706

Bravo

AF:

0.233

Asia WGS

AF:

0.334

AC:

1158

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.4

DANN

Benign

0.76

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