Variant chr11-81260098-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 ENST00000671134.1(ENSG00000287912):n.324-14778A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 151,646 control chromosomes in the GnomAD database, including 54,082 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 0.84 ( 54082 hom., cov: 33)

Consequence

ENSG00000287912
ENST00000671134.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.20

Variant links:

Genes affected

ENSG00000287912 (HGNC:):

ENSG00000287912 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000287912	ENST00000671134.1 link	n.324-14778A>G	intron_variant
ENSG00000287912	ENST00000671210.1 link	n.310-14778A>G	intron_variant
ENSG00000287912	ENST00000701193.1 link	n.114-14778A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.844

AC:

127936

AN:

151528

Hom.:

54045

Cov.:

show subpopulations

Gnomad AFR

AF:

0.848

Gnomad AMI

AF:

0.872

Gnomad AMR

AF:

0.854

Gnomad ASJ

AF:

0.850

Gnomad EAS

AF:

0.971

Gnomad SAS

AF:

0.878

Gnomad FIN

AF:

0.842

Gnomad MID

AF:

0.787

Gnomad NFE

AF:

0.828

Gnomad OTH

AF:

0.824

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

GnomAD4 genome

AF:

0.844

AC:

128026

AN:

151646

Hom.:

54082

Cov.:

AF XY:

0.847

AC XY:

62767

AN XY:

74130

show subpopulations

Gnomad4 AFR

AF:

0.848

Gnomad4 AMR

AF:

0.855

Gnomad4 ASJ

AF:

0.850

Gnomad4 EAS

AF:

0.971

Gnomad4 SAS

AF:

0.878

Gnomad4 FIN

AF:

0.842

Gnomad4 NFE

AF:

0.828

Gnomad4 OTH

AF:

0.822

Alfa

AF:

0.829

Hom.:

65351

Bravo

AF:

0.847

Asia WGS

AF:

0.910

AC:

3166

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.088

DANN

Benign

0.49

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