Variant rs35916350 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 0.099 in 152,430 control chromosomes in the GnomAD database, including 925 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 0.099 ( 921 hom., cov: 33)

Exomes 𝑓: 0.16 ( 4 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.380

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0989

AC:

15050

AN:

152124

Hom.:

919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0386

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.0721

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.0777

Gnomad SAS

AF:

0.0403

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.0994

GnomAD4 exome

AF:

0.160

AC:

AN:

188

Hom.:

AF XY:

0.169

AC XY:

AN XY:

142

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.171

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0989

AC:

15053

AN:

152242

Hom.:

921

Cov.:

AF XY:

0.0979

AC XY:

7286

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0385

Gnomad4 AMR

AF:

0.0721

Gnomad4 ASJ

AF:

0.119

Gnomad4 EAS

AF:

0.0771

Gnomad4 SAS

AF:

0.0403

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.133

Gnomad4 OTH

AF:

0.102

Alfa

AF:

0.107

Hom.:

102

Bravo

AF:

0.0901

Asia WGS

AF:

0.0710

AC:

245

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.4

DANN

Benign

0.62

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