Variant rs7893600 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 0.95 in 151,838 control chromosomes in the GnomAD database, including 69,183 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 0.95 ( 69183 hom., cov: 29)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.406

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.23145815A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.950

AC:

144083

AN:

151720

Hom.:

69136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.957

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.793

Gnomad ASJ

AF:

0.984

Gnomad EAS

AF:

0.592

Gnomad SAS

AF:

0.973

Gnomad FIN

AF:

0.987

Gnomad MID

AF:

0.994

Gnomad NFE

AF:

0.997

Gnomad OTH

AF:

0.948

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

GnomAD4 genome

AF:

0.950

AC:

144183

AN:

151838

Hom.:

69183

Cov.:

AF XY:

0.946

AC XY:

70115

AN XY:

74156

show subpopulations

Gnomad4 AFR

AF:

0.957

Gnomad4 AMR

AF:

0.793

Gnomad4 ASJ

AF:

0.984

Gnomad4 EAS

AF:

0.591

Gnomad4 SAS

AF:

0.973

Gnomad4 FIN

AF:

0.987

Gnomad4 NFE

AF:

0.997

Gnomad4 OTH

AF:

0.948

Alfa

AF:

0.980

Hom.:

127555

Bravo

AF:

0.930

Asia WGS

AF:

0.798

AC:

2777

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.031

DANN

Benign

0.61

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