Variant rs7874183 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 0.282 in 152,154 control chromosomes in the GnomAD database, including 6,778 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 0.28 ( 6778 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.127

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42931

AN:

152036

Hom.:

6775

Cov.:

show subpopulations

Gnomad AFR

AF:

0.351

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.601

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.220

Gnomad OTH

AF:

0.303

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

GnomAD4 genome

AF:

0.282

AC:

42961

AN:

152154

Hom.:

6778

Cov.:

AF XY:

0.285

AC XY:

21188

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.351

Gnomad4 AMR

AF:

0.317

Gnomad4 ASJ

AF:

0.219

Gnomad4 EAS

AF:

0.601

Gnomad4 SAS

AF:

0.442

Gnomad4 FIN

AF:

0.165

Gnomad4 NFE

AF:

0.220

Gnomad4 OTH

AF:

0.301

Alfa

AF:

0.244

Hom.:

4901

Bravo

AF:

0.297

Asia WGS

AF:

0.497

AC:

1725

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.9

DANN

Benign

0.49

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