Variant 6-48545299-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_001744151.1(LOC107986602):n.466+6018A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,898 control chromosomes in the GnomAD database, including 22,897 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 0.54 ( 22897 hom., cov: 31)

Consequence

LOC107986602
XR_001744151.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.481

Variant links:

Genes affected

LOC107986602 (HGNC:):

LOC107986602 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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC107986602	XR_001744151.1 link	n.466+6018A>G	intron_variant
LOC107986602	XR_001744152.1 link	n.234+6018A>G	intron_variant
LOC107986602	XR_001744154.1 link	n.455+6018A>G	intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.537

AC:

81554

AN:

151780

Hom.:

22870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.614

Gnomad AMI

AF:

0.312

Gnomad AMR

AF:

0.628

Gnomad ASJ

AF:

0.496

Gnomad EAS

AF:

0.885

Gnomad SAS

AF:

0.662

Gnomad FIN

AF:

0.465

Gnomad MID

AF:

0.564

Gnomad NFE

AF:

0.452

Gnomad OTH

AF:

0.520

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

GnomAD4 genome

AF:

0.537

AC:

81630

AN:

151898

Hom.:

22897

Cov.:

AF XY:

0.542

AC XY:

40263

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.614

Gnomad4 AMR

AF:

0.629

Gnomad4 ASJ

AF:

0.496

Gnomad4 EAS

AF:

0.885

Gnomad4 SAS

AF:

0.660

Gnomad4 FIN

AF:

0.465

Gnomad4 NFE

AF:

0.452

Gnomad4 OTH

AF:

0.520

Alfa

AF:

0.477

Hom.:

23531

Bravo

AF:

0.552

Asia WGS

AF:

0.710

AC:

2464

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

0.95

DANN

Benign

0.56

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