Variant 4-105143469-TA-TAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XM_047416559.1(LOC124900868):c.*778+2025_*778+2026insT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.51 ( 20534 hom., cov: 0)

Consequence

LOC124900868
XM_047416559.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0460

Variant links:

Genes affected

LOC124900868 (HGNC:):

LOC124900868 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900868	XM_047416559.1 linkuse as main transcript	c.778+2025_778+2026insT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.509

AC:

77095

AN:

151466

Hom.:

20496

Cov.:

show subpopulations

Gnomad AFR

AF:

0.620

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.526

Gnomad ASJ

AF:

0.509

Gnomad EAS

AF:

0.812

Gnomad SAS

AF:

0.588

Gnomad FIN

AF:

0.531

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.408

Gnomad OTH

AF:

0.506

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

GnomAD4 genome

AF:

0.509

AC:

77194

AN:

151584

Hom.:

20534

Cov.:

AF XY:

0.521

AC XY:

38576

AN XY:

74040

show subpopulations

Gnomad4 AFR

AF:

0.620

Gnomad4 AMR

AF:

0.526

Gnomad4 ASJ

AF:

0.509

Gnomad4 EAS

AF:

0.812

Gnomad4 SAS

AF:

0.588

Gnomad4 FIN

AF:

0.531

Gnomad4 NFE

AF:

0.408

Gnomad4 OTH

AF:

0.513

Asia WGS

AF:

0.689

AC:

2389

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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