Variant 11-6321099-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000649129.2(ENSG00000282556):n.558+1402T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,212 control chromosomes in the GnomAD database, including 50,799 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 0.80 ( 50799 hom., cov: 33)

Consequence

ENSG00000282556
ENST00000649129.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.13

Variant links:

Genes affected

ENSG00000282556 (HGNC:):

ENSG00000282556 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC101927825	XR_001748105.3 link	n.557+1402T>G	intron_variant
LOC101927825	XR_001748108.3 link	n.557+1402T>G	intron_variant
LOC101927825	XR_001748109.3 link	n.557+1402T>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000282556	ENST00000649129.2 link	n.558+1402T>G	intron_variant
ENSG00000282556	ENST00000652923.1 link	n.164+1402T>G	intron_variant
ENSG00000282556	ENST00000655261.1 link	n.61+1402T>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.801

AC:

121881

AN:

152094

Hom.:

50795

Cov.:

show subpopulations

Gnomad AFR

AF:

0.547

Gnomad AMI

AF:

0.876

Gnomad AMR

AF:

0.896

Gnomad ASJ

AF:

0.832

Gnomad EAS

AF:

0.916

Gnomad SAS

AF:

0.785

Gnomad FIN

AF:

0.908

Gnomad MID

AF:

0.877

Gnomad NFE

AF:

0.907

Gnomad OTH

AF:

0.824

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

GnomAD4 genome

AF:

0.801

AC:

121933

AN:

152212

Hom.:

50799

Cov.:

AF XY:

0.801

AC XY:

59598

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.547

Gnomad4 AMR

AF:

0.896

Gnomad4 ASJ

AF:

0.832

Gnomad4 EAS

AF:

0.916

Gnomad4 SAS

AF:

0.786

Gnomad4 FIN

AF:

0.908

Gnomad4 NFE

AF:

0.907

Gnomad4 OTH

AF:

0.818

Alfa

AF:

0.886

Hom.:

79038

Bravo

AF:

0.789

Asia WGS

AF:

0.808

AC:

2813

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.1

DANN

Benign

0.55

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