Variant rs9788730 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000560900.1(ENSG00000259754):n.258+26442A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,050 control chromosomes in the GnomAD database, including 9,868 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 0.27 ( 9868 hom., cov: 33)

Consequence

ENSG00000259754
ENST00000560900.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0720

Variant links:

Genes affected

ENSG00000259754 (HGNC:):

ENSG00000259754 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900354	XR_001751516.3 linkuse as main transcript	n.205+26442A>C		intron_variant
LOC124900354	XR_001751518.3 linkuse as main transcript	n.145+26442A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000259754	ENST00000560900.1 linkuse as main transcript	n.258+26442A>C	intron_variant	4
ENSG00000259754	ENST00000662551.1 linkuse as main transcript	n.251+26442A>C	intron_variant
ENSG00000259754	ENST00000665188.1 linkuse as main transcript	n.220+21058A>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40320

AN:

151930

Hom.:

9827

Cov.:

show subpopulations

Gnomad AFR

AF:

0.574

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.0963

Gnomad EAS

AF:

0.825

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.0546

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0821

Gnomad OTH

AF:

0.243

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

GnomAD4 genome

AF:

0.266

AC:

40429

AN:

152050

Hom.:

9868

Cov.:

AF XY:

0.265

AC XY:

19678

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.574

Gnomad4 AMR

AF:

0.283

Gnomad4 ASJ

AF:

0.0963

Gnomad4 EAS

AF:

0.824

Gnomad4 SAS

AF:

0.203

Gnomad4 FIN

AF:

0.0546

Gnomad4 NFE

AF:

0.0821

Gnomad4 OTH

AF:

0.250

Alfa

AF:

0.127

Hom.:

3120

Bravo

AF:

0.303

Asia WGS

AF:

0.539

AC:

1873

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

3.0

DANN

Benign

0.78

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