Variant rs1218117 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.55 ( 12582 hom., 17843 hem., cov: 23)

Failed GnomAD Quality Control

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.28

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.118251602A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.550

AC:

60907

AN:

110723

Hom.:

12590

Cov.:

AF XY:

0.541

AC XY:

17821

AN XY:

32939

show subpopulations

Gnomad AFR

AF:

0.448

Gnomad AMI

AF:

0.540

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.732

Gnomad EAS

AF:

0.318

Gnomad SAS

AF:

0.400

Gnomad FIN

AF:

0.703

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.646

Gnomad OTH

AF:

0.551

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.550

AC:

60911

AN:

110779

Hom.:

12582

Cov.:

AF XY:

0.541

AC XY:

17843

AN XY:

33005

show subpopulations

Gnomad4 AFR

AF:

0.448

Gnomad4 AMR

AF:

0.347

Gnomad4 ASJ

AF:

0.732

Gnomad4 EAS

AF:

0.318

Gnomad4 SAS

AF:

0.400

Gnomad4 FIN

AF:

0.703

Gnomad4 NFE

AF:

0.646

Gnomad4 OTH

AF:

0.549

Alfa

AF:

0.602

Hom.:

6144

Bravo

AF:

0.518

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.64

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