Variant chr1-227469680-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 0.47 in 152,040 control chromosomes in the GnomAD database, including 17,301 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 0.47 ( 17301 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.625

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.470

AC:

71437

AN:

151922

Hom.:

17294

Cov.:

show subpopulations

Gnomad AFR

AF:

0.355

Gnomad AMI

AF:

0.637

Gnomad AMR

AF:

0.516

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.617

Gnomad SAS

AF:

0.392

Gnomad FIN

AF:

0.532

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.511

Gnomad OTH

AF:

0.472

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

GnomAD4 genome

AF:

0.470

AC:

71463

AN:

152040

Hom.:

17301

Cov.:

AF XY:

0.470

AC XY:

34961

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.354

Gnomad4 AMR

AF:

0.517

Gnomad4 ASJ

AF:

0.500

Gnomad4 EAS

AF:

0.617

Gnomad4 SAS

AF:

0.393

Gnomad4 FIN

AF:

0.532

Gnomad4 NFE

AF:

0.511

Gnomad4 OTH

AF:

0.466

Alfa

AF:

0.491

Hom.:

8565

Bravo

AF:

0.469

Asia WGS

AF:

0.470

AC:

1634

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

4.2

DANN

Benign

0.48

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