Variant rs7089102 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 0.516 in 151,808 control chromosomes in the GnomAD database, including 20,440 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 0.52 ( 20440 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.419

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.56086406C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.516

AC:

78289

AN:

151690

Hom.:

20435

Cov.:

show subpopulations

Gnomad AFR

AF:

0.511

Gnomad AMI

AF:

0.491

Gnomad AMR

AF:

0.522

Gnomad ASJ

AF:

0.526

Gnomad EAS

AF:

0.771

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.457

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.506

Gnomad OTH

AF:

0.527

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

GnomAD4 genome

AF:

0.516

AC:

78325

AN:

151808

Hom.:

20440

Cov.:

AF XY:

0.514

AC XY:

38169

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.511

Gnomad4 AMR

AF:

0.522

Gnomad4 ASJ

AF:

0.526

Gnomad4 EAS

AF:

0.771

Gnomad4 SAS

AF:

0.522

Gnomad4 FIN

AF:

0.457

Gnomad4 NFE

AF:

0.506

Gnomad4 OTH

AF:

0.530

Alfa

AF:

0.496

Hom.:

2356

Bravo

AF:

0.519

Asia WGS

AF:

0.631

AC:

2193

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.5

DANN

Benign

0.64

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