Variant rs4016810 details in Genebe, Genetics Data Aggregator

Variant summary

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

The XR_001747415.2(LOC107984219):n.5354-10717_5354-10716del variant causes a intron, non coding transcript 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 0.47 ( 17242 hom., cov: 0)

Consequence

LOC107984219
XR_001747415.2 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0580

Variant links:

Genes affected

LOC107984219 (HGNC:):

LOC107984219 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 = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984219	XR_001747415.2 linkuse as main transcript	n.5354-10717_5354-10716del		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.470

AC:

71056

AN:

151290

Hom.:

17242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.350

Gnomad AMI

AF:

0.540

Gnomad AMR

AF:

0.478

Gnomad ASJ

AF:

0.472

Gnomad EAS

AF:

0.605

Gnomad SAS

AF:

0.493

Gnomad FIN

AF:

0.595

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.470

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

GnomAD4 genome

AF:

0.469

AC:

71079

AN:

151408

Hom.:

17242

Cov.:

AF XY:

0.474

AC XY:

35046

AN XY:

73930

show subpopulations

Gnomad4 AFR

AF:

0.350

Gnomad4 AMR

AF:

0.477

Gnomad4 ASJ

AF:

0.472

Gnomad4 EAS

AF:

0.605

Gnomad4 SAS

AF:

0.495

Gnomad4 FIN

AF:

0.595

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.468

Alfa

AF:

0.492

Hom.:

2269

Bravo

AF:

0.456

Asia WGS

AF:

0.516

AC:

1790

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