Variant rs580831 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000663545.1(ENSG00000287373):n.1153+20335C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.50 ( 12216 hom., cov: 12)

Consequence

ENST00000663545.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.41

Variant links:

Genes affected

(HGNC:):

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=-1.06).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663545.1 linkuse as main transcript	n.1153+20335C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.499

AC:

49948

AN:

100034

Hom.:

12212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.442

Gnomad AMI

AF:

0.553

Gnomad AMR

AF:

0.525

Gnomad ASJ

AF:

0.584

Gnomad EAS

AF:

0.630

Gnomad SAS

AF:

0.616

Gnomad FIN

AF:

0.396

Gnomad MID

AF:

0.586

Gnomad NFE

AF:

0.509

Gnomad OTH

AF:

0.517

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

GnomAD4 genome

AF:

0.499

AC:

49959

AN:

100062

Hom.:

12216

Cov.:

AF XY:

0.494

AC XY:

22955

AN XY:

46438

show subpopulations

Gnomad4 AFR

AF:

0.442

Gnomad4 AMR

AF:

0.525

Gnomad4 ASJ

AF:

0.584

Gnomad4 EAS

AF:

0.630

Gnomad4 SAS

AF:

0.614

Gnomad4 FIN

AF:

0.396

Gnomad4 NFE

AF:

0.509

Gnomad4 OTH

AF:

0.520

Alfa

AF:

0.350

Hom.:

583

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.49

DANN

Benign

0.082

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