rs2855039

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 0.246 in 152,048 control chromosomes in the GnomAD database, including 5,152 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 0.25 ( 5152 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.13
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 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:
0.246
AC:
37348
AN:
151930
Hom.:
5155
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.237
Gnomad AMR
AF:
0.210
Gnomad ASJ
AF:
0.198
Gnomad EAS
AF:
0.118
Gnomad SAS
AF:
0.278
Gnomad FIN
AF:
0.216
Gnomad MID
AF:
0.207
Gnomad NFE
AF:
0.320
Gnomad OTH
AF:
0.252
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.246
AC:
37352
AN:
152048
Hom.:
5152
Cov.:
32
AF XY:
0.241
AC XY:
17889
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.160
Gnomad4 AMR
AF:
0.209
Gnomad4 ASJ
AF:
0.198
Gnomad4 EAS
AF:
0.117
Gnomad4 SAS
AF:
0.278
Gnomad4 FIN
AF:
0.216
Gnomad4 NFE
AF:
0.320
Gnomad4 OTH
AF:
0.253
Alfa
AF:
0.299
Hom.:
13407
Bravo
AF:
0.237
Asia WGS
AF:
0.232
AC:
805
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
0.065
DANN
Benign
0.41

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: rs2855039; hg19: chr11-5271671; API