Variant rs387504 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 0.279 in 151,686 control chromosomes in the GnomAD database, including 6,626 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 0.28 ( 6626 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34

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=-0.96).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.43941836G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42345

AN:

151568

Hom.:

6618

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.382

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.334

Gnomad OTH

AF:

0.320

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

GnomAD4 genome

AF:

0.279

AC:

42360

AN:

151686

Hom.:

6626

Cov.:

AF XY:

0.282

AC XY:

20888

AN XY:

74108

show subpopulations

Gnomad4 AFR

AF:

0.126

Gnomad4 AMR

AF:

0.383

Gnomad4 ASJ

AF:

0.380

Gnomad4 EAS

AF:

0.333

Gnomad4 SAS

AF:

0.262

Gnomad4 FIN

AF:

0.306

Gnomad4 NFE

AF:

0.334

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.307

Hom.:

941

Bravo

AF:

0.280

Asia WGS

AF:

0.268

AC:

930

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.9

DANN

Benign

0.26

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