Variant rs6596684 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 0.603 in 151,892 control chromosomes in the GnomAD database, including 28,693 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 0.60 ( 28693 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.86

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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.106609232G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.604

AC:

91622

AN:

151776

Hom.:

28699

Cov.:

show subpopulations

Gnomad AFR

AF:

0.437

Gnomad AMI

AF:

0.733

Gnomad AMR

AF:

0.655

Gnomad ASJ

AF:

0.616

Gnomad EAS

AF:

0.557

Gnomad SAS

AF:

0.387

Gnomad FIN

AF:

0.706

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.694

Gnomad OTH

AF:

0.594

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

GnomAD4 genome

AF:

0.603

AC:

91622

AN:

151892

Hom.:

28693

Cov.:

AF XY:

0.599

AC XY:

44475

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.437

Gnomad4 AMR

AF:

0.655

Gnomad4 ASJ

AF:

0.616

Gnomad4 EAS

AF:

0.556

Gnomad4 SAS

AF:

0.387

Gnomad4 FIN

AF:

0.706

Gnomad4 NFE

AF:

0.694

Gnomad4 OTH

AF:

0.588

Alfa

AF:

0.661

Hom.:

43298

Bravo

AF:

0.596

Asia WGS

AF:

0.466

AC:

1624

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.12

DANN

Benign

0.56

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