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GeneBe

rs3851179

chr11-86157598-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 0.691 in 151956 control chromosomes in the gnomAD Genomes database, including 36969 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 0.69 ( 36969 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.482

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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:
0.691
AC:
104974
AN:
151956
Hom.:
36969
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.845
Gnomad AMI
AF:
0.521
Gnomad AMR
AF:
0.638
Gnomad ASJ
AF:
0.606
Gnomad EAS
AF:
0.603
Gnomad SAS
AF:
0.610
Gnomad FIN
AF:
0.648
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.635
Gnomad OTH
AF:
0.682
Alfa
AF:
0.639
Hom.:
68346
Bravo
AF:
0.696
Asia WGS
AF:
0.602
AC:
2093
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
5.4
Dann
Benign
0.73

Splicing

Find out SpliceAI 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: rs3851179; hg19: chr11-85868640;