Variant 4-99273964-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000500358.6(ENSG00000246090):n.3790-12831C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,268 control chromosomes in the GnomAD database, including 51,057 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 0.82 ( 51057 hom., cov: 33)

Consequence

ENSG00000246090
ENST00000500358.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.87

Variant links:

Genes affected

ENSG00000246090 (HGNC:):

ENSG00000246090 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1 link	n.3790-12831C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000246090	ENST00000500358.6 link	n.3790-12831C>G	intron_variant	1
ENSG00000246090	ENST00000509295.5 link	n.695-161C>G	intron_variant	1
ENSG00000246090	ENST00000506160.1 link	n.408-4489C>G	intron_variant	4

Frequencies

GnomAD3 genomes

AF:

0.816

AC:

124169

AN:

152150

Hom.:

51004

Cov.:

show subpopulations

Gnomad AFR

AF:

0.910

Gnomad AMI

AF:

0.813

Gnomad AMR

AF:

0.805

Gnomad ASJ

AF:

0.844

Gnomad EAS

AF:

0.911

Gnomad SAS

AF:

0.699

Gnomad FIN

AF:

0.731

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.774

Gnomad OTH

AF:

0.825

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

GnomAD4 genome

AF:

0.816

AC:

124277

AN:

152268

Hom.:

51057

Cov.:

AF XY:

0.811

AC XY:

60390

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.910

Gnomad4 AMR

AF:

0.805

Gnomad4 ASJ

AF:

0.844

Gnomad4 EAS

AF:

0.911

Gnomad4 SAS

AF:

0.700

Gnomad4 FIN

AF:

0.731

Gnomad4 NFE

AF:

0.774

Gnomad4 OTH

AF:

0.821

Alfa

AF:

0.791

Hom.:

5573

Bravo

AF:

0.830

Asia WGS

AF:

0.748

AC:

2599

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.043

DANN

Benign

0.57

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