Variant rs35598594 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.107 in 152,188 control chromosomes in the GnomAD database, including 1,163 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1163 hom., cov: 30)

Consequence

intergenic_region

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.478

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.27594724_27594725insT		intergenic_region
LOC124901919	XR_007060868.1 linkuse as main transcript	n.1397+2113dupT		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16279

AN:

152070

Hom.:

1163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0279

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0920

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.121

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

GnomAD4 genome

AF:

0.107

AC:

16285

AN:

152188

Hom.:

1163

Cov.:

AF XY:

0.104

AC XY:

7727

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.0278

Gnomad4 AMR

AF:

0.100

Gnomad4 ASJ

AF:

0.177

Gnomad4 EAS

AF:

0.000965

Gnomad4 SAS

AF:

0.0929

Gnomad4 FIN

AF:

0.123

Gnomad4 NFE

AF:

0.160

Gnomad4 OTH

AF:

0.120

Alfa

AF:

0.132

Hom.:

189

Bravo

AF:

0.101

Asia WGS

AF:

0.0370

AC:

128

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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