Variant 1-23869911-A-G 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 0.634 in 151,468 control chromosomes in the GnomAD database, including 30,851 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 0.63 ( 30851 hom., cov: 28)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.23869911A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.634

AC:

95974

AN:

151350

Hom.:

30841

Cov.:

show subpopulations

Gnomad AFR

AF:

0.757

Gnomad AMI

AF:

0.548

Gnomad AMR

AF:

0.640

Gnomad ASJ

AF:

0.580

Gnomad EAS

AF:

0.525

Gnomad SAS

AF:

0.713

Gnomad FIN

AF:

0.575

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.619

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

GnomAD4 genome

AF:

0.634

AC:

96026

AN:

151468

Hom.:

30851

Cov.:

AF XY:

0.637

AC XY:

47119

AN XY:

73960

show subpopulations

Gnomad4 AFR

AF:

0.756

Gnomad4 AMR

AF:

0.640

Gnomad4 ASJ

AF:

0.580

Gnomad4 EAS

AF:

0.524

Gnomad4 SAS

AF:

0.713

Gnomad4 FIN

AF:

0.575

Gnomad4 NFE

AF:

0.574

Gnomad4 OTH

AF:

0.613

Alfa

AF:

0.592

Hom.:

27028

Bravo

AF:

0.644

Asia WGS

AF:

0.630

AC:

2191

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.81

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