rs2879278

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 0.328 in 151,972 control chromosomes in the GnomAD database, including 8,877 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 0.33 ( 8877 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.57
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=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 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:
0.328
AC:
49822
AN:
151854
Hom.:
8881
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.177
Gnomad AMI
AF:
0.471
Gnomad AMR
AF:
0.359
Gnomad ASJ
AF:
0.366
Gnomad EAS
AF:
0.329
Gnomad SAS
AF:
0.331
Gnomad FIN
AF:
0.320
Gnomad MID
AF:
0.261
Gnomad NFE
AF:
0.411
Gnomad OTH
AF:
0.306
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.328
AC:
49807
AN:
151972
Hom.:
8877
Cov.:
32
AF XY:
0.326
AC XY:
24218
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.177
Gnomad4 AMR
AF:
0.358
Gnomad4 ASJ
AF:
0.366
Gnomad4 EAS
AF:
0.330
Gnomad4 SAS
AF:
0.330
Gnomad4 FIN
AF:
0.320
Gnomad4 NFE
AF:
0.411
Gnomad4 OTH
AF:
0.302
Alfa
AF:
0.388
Hom.:
8098
Bravo
AF:
0.323
Asia WGS
AF:
0.314
AC:
1088
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.64
DANN
Benign
0.95

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: rs2879278; hg19: chr5-169572731; API