Variant 3-117509776-GTGGGAATTTGAATATTATAACAGATCC-GTGGGAATTTGAATATTATAACAGATCCTGGGAATTTGAATATTATAACAGATCC details in Genebe, Genetics Data Aggregator

Variant summary

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

The XR_924361.3(LOC105374056):n.26459_26485dup 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 0.391 in 150,732 control chromosomes in the GnomAD database, including 14,183 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 14183 hom., cov: 24)

Consequence

LOC105374056
XR_924361.3 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.787

Variant links:

Genes affected

LOC105374056 (HGNC:):

LOC105374056 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374056	XR_924361.3 linkuse as main transcript	n.26459_26485dup		non_coding_transcript_exon_variant	1/4
LOC105374056	XR_007096021.1 linkuse as main transcript	n.26459_26485dup		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

58930

AN:

150616

Hom.:

14188

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.325

Gnomad ASJ

AF:

0.514

Gnomad EAS

AF:

0.214

Gnomad SAS

AF:

0.438

Gnomad FIN

AF:

0.489

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.557

Gnomad OTH

AF:

0.407

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

GnomAD4 genome

AF:

0.391

AC:

58904

AN:

150732

Hom.:

14183

Cov.:

AF XY:

0.385

AC XY:

28309

AN XY:

73558

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.325

Gnomad4 ASJ

AF:

0.514

Gnomad4 EAS

AF:

0.213

Gnomad4 SAS

AF:

0.438

Gnomad4 FIN

AF:

0.489

Gnomad4 NFE

AF:

0.557

Gnomad4 OTH

AF:

0.403

Alfa

AF:

0.374

Hom.:

1322

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