Variant chr4-89687808-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The XR_007058465.1(LOC124900602):n.6304C>T 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 0.26 in 152,126 control chromosomes in the GnomAD database, including 9,036 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 0.26 ( 9036 hom., cov: 33)

Consequence

LOC124900602
XR_007058465.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0170

Variant links:

Genes affected

LOC124900602 (HGNC:):

LOC124900602 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LOC124900602	XR_007058465.1 link	n.6304C>T	non_coding_transcript_exon_variant	1/2
LOC124900602	XR_007058466.1 link	n.6304C>T	non_coding_transcript_exon_variant	1/3
LOC124900602	XR_001741764.2 link	n.5498+806C>T	intron_variant
LOC124900602	XR_938983.2 link	n.5498+806C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000251095	ENST00000506864.5 link	n.472-3477C>T	intron_variant	4
ENSG00000251095	ENST00000507916.6 link	n.135-3477C>T	intron_variant	3
ENSG00000251095	ENST00000508021.5 link	n.327-3477C>T	intron_variant	4

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39457

AN:

152008

Hom.:

9007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.624

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.180

Gnomad EAS

AF:

0.0673

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.231

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

GnomAD4 genome

AF:

0.260

AC:

39534

AN:

152126

Hom.:

9036

Cov.:

AF XY:

0.255

AC XY:

18936

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.624

Gnomad4 AMR

AF:

0.134

Gnomad4 ASJ

AF:

0.180

Gnomad4 EAS

AF:

0.0675

Gnomad4 SAS

AF:

0.103

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.120

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.157

Hom.:

2372

Bravo

AF:

0.275

Asia WGS

AF:

0.135

AC:

469

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.2

DANN

Benign

0.53

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