Variant rs1884302 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 0.403 in 152,046 control chromosomes in the GnomAD database, including 13,510 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.40 ( 13510 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -0.424

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) 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
	use as main transcript	n.7125642T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000232271	ENST00000425900.1 linkuse as main transcript	n.82-20715T>C		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61119

AN:

151928

Hom.:

13477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.593

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.432

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.382

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

GnomAD4 genome

AF:

0.403

AC:

61217

AN:

152046

Hom.:

13510

Cov.:

AF XY:

0.399

AC XY:

29641

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.594

Gnomad4 AMR

AF:

0.380

Gnomad4 ASJ

AF:

0.316

Gnomad4 EAS

AF:

0.432

Gnomad4 SAS

AF:

0.237

Gnomad4 FIN

AF:

0.338

Gnomad4 NFE

AF:

0.319

Gnomad4 OTH

AF:

0.384

Alfa

AF:

0.337

Hom.:

11665

Bravo

AF:

0.416

Asia WGS

AF:

0.375

AC:

1305

AN:

3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Craniosynostosis 7

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Feb 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.7

DANN

Benign

0.61

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over