Variant rs1918526 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 0.89 in 152,242 control chromosomes in the GnomAD database, including 62,054 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 0.89 ( 62054 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.556

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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.115497954G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.891

AC:

135467

AN:

152124

Hom.:

62032

Cov.:

show subpopulations

Gnomad AFR

AF:

0.649

Gnomad AMI

AF:

0.992

Gnomad AMR

AF:

0.946

Gnomad ASJ

AF:

0.974

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.934

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.905

Gnomad NFE

AF:

0.991

Gnomad OTH

AF:

0.899

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

GnomAD4 genome

AF:

0.890

AC:

135544

AN:

152242

Hom.:

62054

Cov.:

AF XY:

0.894

AC XY:

66528

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.649

Gnomad4 AMR

AF:

0.947

Gnomad4 ASJ

AF:

0.974

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.934

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.991

Gnomad4 OTH

AF:

0.900

Alfa

AF:

0.918

Hom.:

10718

Bravo

AF:

0.875

Asia WGS

AF:

0.945

AC:

3286

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.43

DANN

Benign

0.39

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