Variant rs3138035 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 0.274 in 152,358 control chromosomes in the GnomAD database, including 6,739 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 0.27 ( 6726 hom., cov: 33)

Exomes 𝑓: 0.38 ( 13 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.92

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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.34318930C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41600

AN:

152022

Hom.:

6726

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.287

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.363

Gnomad EAS

AF:

0.0953

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.414

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.368

Gnomad OTH

AF:

0.274

GnomAD4 exome

AF:

0.375

AC:

AN:

216

Hom.:

AF XY:

0.331

AC XY:

AN XY:

118

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.355

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.405

GnomAD4 genome

AF:

0.273

AC:

41596

AN:

152142

Hom.:

6726

Cov.:

AF XY:

0.274

AC XY:

20383

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.218

Gnomad4 ASJ

AF:

0.363

Gnomad4 EAS

AF:

0.0954

Gnomad4 SAS

AF:

0.242

Gnomad4 FIN

AF:

0.414

Gnomad4 NFE

AF:

0.368

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.337

Hom.:

12110

Bravo

AF:

0.249

Asia WGS

AF:

0.151

AC:

529

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.057

DANN

Benign

0.45

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