Variant chr1-4560936-C-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 0.207 in 152,026 control chromosomes in the GnomAD database, including 3,380 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 0.21 ( 3380 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.85

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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 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:

0.207

AC:

31511

AN:

151908

Hom.:

3381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.314

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.263

Gnomad EAS

AF:

0.0110

Gnomad SAS

AF:

0.234

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.224

Gnomad OTH

AF:

0.197

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

GnomAD4 genome

AF:

0.207

AC:

31522

AN:

152026

Hom.:

3380

Cov.:

AF XY:

0.209

AC XY:

15527

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.197

Gnomad4 AMR

AF:

0.169

Gnomad4 ASJ

AF:

0.263

Gnomad4 EAS

AF:

0.0111

Gnomad4 SAS

AF:

0.235

Gnomad4 FIN

AF:

0.254

Gnomad4 NFE

AF:

0.224

Gnomad4 OTH

AF:

0.195

Alfa

AF:

0.214

Hom.:

7242

Bravo

AF:

0.200

Asia WGS

AF:

0.128

AC:

447

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

0.15

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