rs2736191

Positions:

• chr6-31593133-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5 BP4 BA1

The variant allele was found at a frequency of 0.106 in 291,288 control chromosomes in the GnomAD database, including 3,609 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic,risk factor (no stars).

• Frequency:
  • Genomes: 𝑓 0.13 (2297 hom., cov: 30)
  • Exomes 𝑓: 0.079 (1312 hom.)
• Consequence: intergenic_region
• Clinical Significance: Pathogenic; risk factor no assertion criteria provided P:1 O:1
• Conservation: PhyloP100: 0.621

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP5: Variant 6-31593133-C-G is Pathogenic according to our data. Variant chr6-31593133-C-G is described in ClinVar as [Pathogenic, risk_factor]. Clinvar id is 876.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67). . Strength limited to SUPPORTING due to the PP5.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31593133C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19678 AN: 151752 Hom.: 2295 Cov.: 30

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.0793 AC: 11054 AN: 139418 Hom.: 1312 AF XY: 0.0785 AC XY: 5732 AN XY: 73036

Gnomad4 AFR exome AF: 0.264

Gnomad4 AMR exome AF: 0.177

Gnomad4 ASJ exome AF: 0.0298

Gnomad4 EAS exome AF: 0.398

Gnomad4 SAS exome AF: 0.0828

Gnomad4 FIN exome AF: 0.0390

Gnomad4 NFE exome AF: 0.0274

Gnomad4 OTH exome AF: 0.0676

GnomAD4 genome AF: 0.130 AC: 19707 AN: 151870 Hom.: 2297 Cov.: 30 AF XY: 0.133 AC XY: 9846 AN XY: 74208

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0499

Gnomad4 NFE AF: 0.0324

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0779 Hom.: 149

Bravo AF: 0.147

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Significance: Pathogenic; risk factor

Submissions summary: Pathogenic:1 Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Malaria, severe, susceptibility to Pathogenic:1

Pathogenic, no assertion criteria provided

research

Center for Global Health, University of New Mexico Health Sciences Center, University of New Mexico

Dec 06, 2022

CC is wild type in the Luo (Kenya) population, GG is homozygous mutant. Additive model of inheritance shows increased susceptibility to longitudinal (over 36 months) severe malarial anemia (Hb<5.0 g/dL with any density Plasmodium falciparum parasitemia) in children <48 months of age. -

Malaria, mild, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Feb 01, 2007

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.5
DANN	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2736191; hg19: chr6-31560910;