Variant chr1-8312476-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 0.553 in 152,060 control chromosomes in the GnomAD database, including 25,107 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 0.55 ( 25107 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.538

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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 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:

0.553

AC:

84046

AN:

151942

Hom.:

25102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.696

Gnomad AMR

AF:

0.642

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.754

Gnomad SAS

AF:

0.490

Gnomad FIN

AF:

0.732

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.638

Gnomad OTH

AF:

0.542

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

GnomAD4 genome

AF:

0.553

AC:

84071

AN:

152060

Hom.:

25107

Cov.:

AF XY:

0.559

AC XY:

41521

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.316

Gnomad4 AMR

AF:

0.642

Gnomad4 ASJ

AF:

0.542

Gnomad4 EAS

AF:

0.754

Gnomad4 SAS

AF:

0.488

Gnomad4 FIN

AF:

0.732

Gnomad4 NFE

AF:

0.638

Gnomad4 OTH

AF:

0.542

Alfa

AF:

0.591

Hom.:

13207

Bravo

AF:

0.541

Asia WGS

AF:

0.554

AC:

1926

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.023

DANN

Benign

0.70

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