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GeneBe

rs361525

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 0.049 in 486,092 control chromosomes in the GnomAD database, including 705 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.047 ( 188 hom., cov: 31)
Exomes 𝑓: 0.050 ( 517 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Uncertain significance no assertion criteria provided U:2

Conservation

PhyloP100: -0.395
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=-0.78).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0588 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:
0.0468
AC:
7114
AN:
152078
Hom.:
187
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0400
Gnomad AMI
AF:
0.154
Gnomad AMR
AF:
0.0504
Gnomad ASJ
AF:
0.0700
Gnomad EAS
AF:
0.0277
Gnomad SAS
AF:
0.0655
Gnomad FIN
AF:
0.0135
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.0522
Gnomad OTH
AF:
0.0650
GnomAD4 exome
AF:
0.0500
AC:
16688
AN:
333896
Hom.:
517
AF XY:
0.0507
AC XY:
9536
AN XY:
188190
show subpopulations
Gnomad4 AFR exome
AF:
0.0408
Gnomad4 AMR exome
AF:
0.0506
Gnomad4 ASJ exome
AF:
0.0745
Gnomad4 EAS exome
AF:
0.0235
Gnomad4 SAS exome
AF:
0.0590
Gnomad4 FIN exome
AF:
0.0171
Gnomad4 NFE exome
AF:
0.0500
Gnomad4 OTH exome
AF:
0.0524
GnomAD4 genome
AF:
0.0468
AC:
7129
AN:
152196
Hom.:
188
Cov.:
31
AF XY:
0.0463
AC XY:
3443
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.0404
Gnomad4 AMR
AF:
0.0504
Gnomad4 ASJ
AF:
0.0700
Gnomad4 EAS
AF:
0.0278
Gnomad4 SAS
AF:
0.0648
Gnomad4 FIN
AF:
0.0135
Gnomad4 NFE
AF:
0.0521
Gnomad4 OTH
AF:
0.0643
Alfa
AF:
0.0530
Hom.:
272
Bravo
AF:
0.0484
Asia WGS
AF:
0.0440
AC:
154
AN:
3478

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Susceptibility to severe coronavirus disease (COVID-19) Uncertain:1
Uncertain significance, no assertion criteria providedresearchHLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio VillegasFeb 09, 2021- -
Susceptibility to severe coronavirus disease (COVID-19) due to high plasma levels of TNF, TNFR, and/or TNFR5 Uncertain:1
Uncertain significance, no assertion criteria providedresearchHLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio VillegasAug 07, 2021Differences in plasma levels of TNFR2 according to genotypes -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
Cadd
Benign
10
Dann
Benign
0.84

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: rs361525; hg19: chr6-31543101; API