Variant rs267413 details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.371 in 152,142 control chromosomes in the GnomAD database, including 11,865 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 0.37 ( 11865 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.696

Variant links:

Genes affected

(HGNC:):

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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.175448605A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.372

AC:

56479

AN:

152022

Hom.:

11856

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.457

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.446

Gnomad SAS

AF:

0.313

Gnomad FIN

AF:

0.478

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.457

Gnomad OTH

AF:

0.387

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

GnomAD4 genome

AF:

0.371

AC:

56509

AN:

152142

Hom.:

11865

Cov.:

AF XY:

0.374

AC XY:

27834

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.171

Gnomad4 AMR

AF:

0.439

Gnomad4 ASJ

AF:

0.405

Gnomad4 EAS

AF:

0.447

Gnomad4 SAS

AF:

0.313

Gnomad4 FIN

AF:

0.478

Gnomad4 NFE

AF:

0.457

Gnomad4 OTH

AF:

0.390

Alfa

AF:

0.408

Hom.:

1714

Bravo

AF:

0.360

Asia WGS

AF:

0.376

AC:

1303

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.9

DANN

Benign

0.63

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