Variant rs1792745 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000590589.2(ENSG00000267732):n.139T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,174 control chromosomes in the GnomAD database, including 54,114 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 ( 54114 hom., cov: 32)

Consequence

ENSG00000267732
ENST00000590589.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.95

Variant links:

Genes affected

ENSG00000267732 (HGNC:):

ENSG00000267732 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LOC105372132	XR_007066384.1 linkuse as main transcript	n.169T>C	non_coding_transcript_exon_variant	1/3
LOC105372132	XR_007066385.1 linkuse as main transcript	n.169T>C	non_coding_transcript_exon_variant	1/3
LOC105372132	XR_007066386.1 linkuse as main transcript	n.23T>C	non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ENSG00000267732	ENST00000590589.2 linkuse as main transcript	n.139T>C	non_coding_transcript_exon_variant	1/3	2
ENSG00000267732	ENST00000654480.1 linkuse as main transcript	n.190T>C	non_coding_transcript_exon_variant	1/3
ENSG00000267732	ENST00000659946.1 linkuse as main transcript	n.105T>C	non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes

AF:

0.836

AC:

127160

AN:

152056

Hom.:

54070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.903

Gnomad AMI

AF:

0.850

Gnomad AMR

AF:

0.696

Gnomad ASJ

AF:

0.861

Gnomad EAS

AF:

0.389

Gnomad SAS

AF:

0.700

Gnomad FIN

AF:

0.851

Gnomad MID

AF:

0.911

Gnomad NFE

AF:

0.866

Gnomad OTH

AF:

0.838

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

GnomAD4 genome

AF:

0.836

AC:

127254

AN:

152174

Hom.:

54114

Cov.:

AF XY:

0.828

AC XY:

61615

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.904

Gnomad4 AMR

AF:

0.695

Gnomad4 ASJ

AF:

0.861

Gnomad4 EAS

AF:

0.389

Gnomad4 SAS

AF:

0.701

Gnomad4 FIN

AF:

0.851

Gnomad4 NFE

AF:

0.866

Gnomad4 OTH

AF:

0.833

Alfa

AF:

0.851

Hom.:

72674

Bravo

AF:

0.824

Asia WGS

AF:

0.564

AC:

1962

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.087

DANN

Benign

0.40

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