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GeneBe

rs2660753

chr3-87061524-T-C

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 0.761 in 151936 control chromosomes in the gnomAD Genomes database, including 46491 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 0.76 ( 46491 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.761
AC:
115690
AN:
151936
Hom.:
46491
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.486
Gnomad AMI
AF:
0.889
Gnomad AMR
AF:
0.825
Gnomad ASJ
AF:
0.779
Gnomad EAS
AF:
0.743
Gnomad SAS
AF:
0.763
Gnomad FIN
AF:
0.926
Gnomad MID
AF:
0.725
Gnomad NFE
AF:
0.888
Gnomad OTH
AF:
0.775
Alfa
AF:
0.860
Hom.:
129035
Bravo
AF:
0.741
Asia WGS
AF:
0.717
AC:
2494
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
7.2
Dann
Benign
0.37

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.

Other links and lift over

dbSNP: rs2660753; hg19: chr3-87110674;