Variant 6-23871472-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 0.314 in 151,784 control chromosomes in the GnomAD database, including 7,816 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 0.31 ( 7816 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.547

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 = 0.362 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:

0.314

AC:

47688

AN:

151668

Hom.:

7807

Cov.:

show subpopulations

Gnomad AFR

AF:

0.361

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.0788

Gnomad SAS

AF:

0.375

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.323

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

GnomAD4 genome

AF:

0.314

AC:

47731

AN:

151784

Hom.:

7816

Cov.:

AF XY:

0.314

AC XY:

23255

AN XY:

74154

show subpopulations

Gnomad4 AFR

AF:

0.361

Gnomad4 AMR

AF:

0.233

Gnomad4 ASJ

AF:

0.310

Gnomad4 EAS

AF:

0.0789

Gnomad4 SAS

AF:

0.376

Gnomad4 FIN

AF:

0.324

Gnomad4 NFE

AF:

0.318

Gnomad4 OTH

AF:

0.323

Alfa

AF:

0.318

Hom.:

984

Bravo

AF:

0.305

Asia WGS

AF:

0.240

AC:

827

AN:

3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.21

DANN

Benign

0.20

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