Variant rs4903696 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 0.512 in 152,072 control chromosomes in the GnomAD database, including 20,565 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 0.51 ( 20565 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0860

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.78050017C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.512

AC:

77756

AN:

151954

Hom.:

20530

Cov.:

show subpopulations

Gnomad AFR

AF:

0.619

Gnomad AMI

AF:

0.511

Gnomad AMR

AF:

0.442

Gnomad ASJ

AF:

0.394

Gnomad EAS

AF:

0.764

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.526

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.521

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

GnomAD4 genome

AF:

0.512

AC:

77849

AN:

152072

Hom.:

20565

Cov.:

AF XY:

0.513

AC XY:

38104

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.619

Gnomad4 AMR

AF:

0.442

Gnomad4 ASJ

AF:

0.394

Gnomad4 EAS

AF:

0.765

Gnomad4 SAS

AF:

0.429

Gnomad4 FIN

AF:

0.526

Gnomad4 NFE

AF:

0.453

Gnomad4 OTH

AF:

0.521

Alfa

AF:

0.466

Hom.:

8025

Bravo

AF:

0.514

Asia WGS

AF:

0.602

AC:

2091

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.93

DANN

Benign

0.29

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