Variant rs3037354 details in Genebe, Genetics Data Aggregator

Variant summary

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

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 6174 hom., cov: 19)

Consequence

intergenic_region

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.796

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
	use as main transcript	n.24283307_24283308delTG	intergenic_region
LOC107986777	XR_001745121.2 linkuse as main transcript	n.209+36049_209+36050delCA	intron_variant
LOC107986777	XR_001745122.2 linkuse as main transcript	n.81-86279_81-86278delCA	intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42663

AN:

151926

Hom.:

6166

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.403

Gnomad AMR

AF:

0.223

Gnomad ASJ

AF:

0.245

Gnomad EAS

AF:

0.308

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.251

Gnomad MID

AF:

0.303

Gnomad NFE

AF:

0.257

Gnomad OTH

AF:

0.285

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

GnomAD4 genome

AF:

0.281

AC:

42692

AN:

152044

Hom.:

6174

Cov.:

AF XY:

0.280

AC XY:

20794

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.343

Gnomad4 AMR

AF:

0.223

Gnomad4 ASJ

AF:

0.245

Gnomad4 EAS

AF:

0.309

Gnomad4 SAS

AF:

0.298

Gnomad4 FIN

AF:

0.251

Gnomad4 NFE

AF:

0.257

Gnomad4 OTH

AF:

0.285

Alfa

AF:

0.268

Hom.:

710

Bravo

AF:

0.281

Asia WGS

AF:

0.310

AC:

1076

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