rs1800750

chr6-31575186-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BS1_Supporting BS2

The variant allele was found at a frequency of 0.0135 in 453,414 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency:
  • Genomes: 𝑓 0.016 (35 hom., cov: 31)
  • Exomes 𝑓: 0.012 (45 hom.)
• Consequence: Unknown
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: 0.557

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0162 (2466/152290) while in subpopulation AMR AF= 0.0256 (392/15292). AF 95% confidence interval is 0.0235. There are 35 homozygotes in gnomad4. There are 1175 alleles in male gnomad4 subpopulation. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Homozygotes in GnomAd at 35 gene

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: 0.0161 AC: 2453 AN: 152172 Hom.: 35 Cov.: 31

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.00310

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0147

Gnomad OTH AF: 0.0307

GnomAD4 exome AF: 0.0121 AC: 3634 AN: 301124 Hom.: 45 AF XY: 0.0112 AC XY: 1916 AN XY: 171752

Gnomad4 AFR exome AF: 0.0191

Gnomad4 AMR exome AF: 0.0229

Gnomad4 ASJ exome AF: 0.0228

Gnomad4 EAS exome AF: 0.000323

Gnomad4 SAS exome AF: 0.00546

Gnomad4 FIN exome AF: 0.00331

Gnomad4 NFE exome AF: 0.0126

Gnomad4 OTH exome AF: 0.0148

GnomAD4 genome AF: 0.0162 AC: 2466 AN: 152290 Hom.: 35 Cov.: 31 AF XY: 0.0158 AC XY: 1175 AN XY: 74468

Gnomad4 AFR AF: 0.0211

Gnomad4 AMR AF: 0.0256

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.00331

Gnomad4 FIN AF: 0.00160

Gnomad4 NFE AF: 0.0147

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0157 Hom.: 38

Bravo AF: 0.0179

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Malaria, cerebral, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jun 01, 1999

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.9
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800750; hg19: chr6-31542963;