Variant rs5930667 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 0.311 in 110,410 control chromosomes in the GnomAD database, including 4,247 homozygotes. There are 9,949 hemizygotes in GnomAD. 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 0.31 ( 4247 hom., 9949 hem., cov: 22)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.134932569C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

34341

AN:

110356

Hom.:

4241

Cov.:

AF XY:

0.304

AC XY:

9926

AN XY:

32640

show subpopulations

Gnomad AFR

AF:

0.419

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.330

Gnomad ASJ

AF:

0.332

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.357

Gnomad FIN

AF:

0.232

Gnomad MID

AF:

0.267

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.324

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

GnomAD4 genome

AF:

0.311

AC:

34374

AN:

110410

Hom.:

4247

Cov.:

AF XY:

0.304

AC XY:

9949

AN XY:

32704

show subpopulations

Gnomad4 AFR

AF:

0.419

Gnomad4 AMR

AF:

0.330

Gnomad4 ASJ

AF:

0.332

Gnomad4 EAS

AF:

0.536

Gnomad4 SAS

AF:

0.358

Gnomad4 FIN

AF:

0.232

Gnomad4 NFE

AF:

0.237

Gnomad4 OTH

AF:

0.332

Alfa

AF:

0.262

Hom.:

8224

Bravo

AF:

0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.6

DANN

Benign

0.86

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