Variant rs4660456 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.218 in 152,214 control chromosomes in the GnomAD database, including 4,278 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 0.22 ( 4278 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0240

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 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:

0.218

AC:

33130

AN:

152096

Hom.:

4269

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.418

Gnomad SAS

AF:

0.420

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.239

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

GnomAD4 genome

AF:

0.218

AC:

33151

AN:

152214

Hom.:

4278

Cov.:

AF XY:

0.224

AC XY:

16651

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.100

Gnomad4 AMR

AF:

0.338

Gnomad4 ASJ

AF:

0.243

Gnomad4 EAS

AF:

0.417

Gnomad4 SAS

AF:

0.418

Gnomad4 FIN

AF:

0.225

Gnomad4 NFE

AF:

0.227

Gnomad4 OTH

AF:

0.246

Alfa

AF:

0.232

Hom.:

5150

Bravo

AF:

0.216

Asia WGS

AF:

0.425

AC:

1477

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

DANN

Benign

0.75

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