rs1879352

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 0.112 in 152,252 control chromosomes in the GnomAD database, including 1,238 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 0.11 ( 1238 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.274
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 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:
0.112
AC:
17001
AN:
152134
Hom.:
1235
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0424
Gnomad AMI
AF:
0.0650
Gnomad AMR
AF:
0.119
Gnomad ASJ
AF:
0.150
Gnomad EAS
AF:
0.0476
Gnomad SAS
AF:
0.120
Gnomad FIN
AF:
0.0887
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.158
Gnomad OTH
AF:
0.131
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.112
AC:
17007
AN:
152252
Hom.:
1238
Cov.:
32
AF XY:
0.109
AC XY:
8130
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0424
Gnomad4 AMR
AF:
0.118
Gnomad4 ASJ
AF:
0.150
Gnomad4 EAS
AF:
0.0477
Gnomad4 SAS
AF:
0.121
Gnomad4 FIN
AF:
0.0887
Gnomad4 NFE
AF:
0.158
Gnomad4 OTH
AF:
0.132
Alfa
AF:
0.147
Hom.:
3305
Bravo
AF:
0.112
Asia WGS
AF:
0.0890
AC:
308
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
7.5
DANN
Benign
0.56

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: rs1879352; hg19: chr18-2498054; API