rs361525

chr6-31575324-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Uncertain significance no assertion criteria provided U:2
• Conservation: PhyloP100: -0.395

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

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

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

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

Submissions by phenotype

Susceptibility to severe coronavirus disease (COVID-19) Uncertain:1

Uncertain significance, no assertion criteria provided

research

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Feb 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 provided

research

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Aug 07, 2021

Differences 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

Other links and lift over

dbSNP: rs361525; hg19: chr6-31543101;