Variant chr1-26102373-G-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 0.231 in 152,090 control chromosomes in the GnomAD database, including 5,294 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 ( 5294 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.213

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 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:

0.231

AC:

35098

AN:

151972

Hom.:

5283

Cov.:

show subpopulations

Gnomad AFR

AF:

0.421

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.203

Gnomad EAS

AF:

0.0172

Gnomad SAS

AF:

0.0813

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.280

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.233

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

GnomAD4 genome

AF:

0.231

AC:

35142

AN:

152090

Hom.:

5294

Cov.:

AF XY:

0.223

AC XY:

16597

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.421

Gnomad4 AMR

AF:

0.161

Gnomad4 ASJ

AF:

0.203

Gnomad4 EAS

AF:

0.0168

Gnomad4 SAS

AF:

0.0804

Gnomad4 FIN

AF:

0.147

Gnomad4 NFE

AF:

0.173

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.183

Hom.:

1632

Bravo

AF:

0.242

Asia WGS

AF:

0.0890

AC:

311

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.3

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