Variant chr1-163063052-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 0.429 in 151,924 control chromosomes in the GnomAD database, including 13,986 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 0.43 ( 13986 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.276

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 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:

0.428

AC:

65037

AN:

151806

Hom.:

13967

Cov.:

show subpopulations

Gnomad AFR

AF:

0.458

Gnomad AMI

AF:

0.399

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.394

Gnomad EAS

AF:

0.437

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.420

Gnomad OTH

AF:

0.441

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

GnomAD4 genome

AF:

0.429

AC:

65116

AN:

151924

Hom.:

13986

Cov.:

AF XY:

0.429

AC XY:

31838

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.458

Gnomad4 AMR

AF:

0.405

Gnomad4 ASJ

AF:

0.394

Gnomad4 EAS

AF:

0.437

Gnomad4 SAS

AF:

0.491

Gnomad4 FIN

AF:

0.378

Gnomad4 NFE

AF:

0.420

Gnomad4 OTH

AF:

0.442

Alfa

AF:

0.421

Hom.:

2524

Bravo

AF:

0.429

Asia WGS

AF:

0.489

AC:

1700

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.6

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