Variant 2-48156607-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000447571.5(ENSG00000230773):n.240+8281C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,734 control chromosomes in the GnomAD database, including 20,914 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 0.51 ( 20914 hom., cov: 30)

Consequence

ENSG00000230773
ENST00000447571.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252

Variant links:

Genes affected

ENSG00000230773 (HGNC:):

ENSG00000230773 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374593	XR_001739456.2 link	n.397+8281C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000230773	ENST00000447571.5 link	n.240+8281C>A	intron_variant	1
ENSG00000230773	ENST00000587616.1 link	n.47+8281C>A	intron_variant	5
ENSG00000230773	ENST00000649883.1 link	n.68-7499C>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.509

AC:

77179

AN:

151616

Hom.:

20911

Cov.:

show subpopulations

Gnomad AFR

AF:

0.612

Gnomad AMI

AF:

0.544

Gnomad AMR

AF:

0.504

Gnomad ASJ

AF:

0.540

Gnomad EAS

AF:

0.954

Gnomad SAS

AF:

0.716

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.497

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

GnomAD4 genome

AF:

0.509

AC:

77230

AN:

151734

Hom.:

20914

Cov.:

AF XY:

0.514

AC XY:

38105

AN XY:

74136

show subpopulations

Gnomad4 AFR

AF:

0.612

Gnomad4 AMR

AF:

0.503

Gnomad4 ASJ

AF:

0.540

Gnomad4 EAS

AF:

0.954

Gnomad4 SAS

AF:

0.714

Gnomad4 FIN

AF:

0.353

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.500

Alfa

AF:

0.450

Hom.:

31865

Bravo

AF:

0.524

Asia WGS

AF:

0.808

AC:

2811

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

2.0

DANN

Benign

0.50

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