rs1800750

Variant names:

• chr6-31575186-G-A
• rs1800750

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 31. This position FAILED quality control check. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Homozygotes in GnomAd4 at 35 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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 AC: 162 AN: 8474

Gnomad4 AMR exome AF: 0.0229 AC: 604 AN: 26370

Gnomad4 ASJ exome AF: 0.0228 AC: 241 AN: 10550

Gnomad4 EAS exome AF: 0.000323 AC: 3 AN: 9278

Gnomad4 SAS exome AF: 0.00546 AC: 322 AN: 58952

Gnomad4 FIN exome AF: 0.00331 AC: 43 AN: 13010

Gnomad4 NFE exome AF: 0.0126 AC: 1989 AN: 157496

Gnomad4 Remaining exome AF: 0.0148 AC: 211 AN: 14214

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 AC: 0.021079 AN: 0.021079

Gnomad4 AMR AF: 0.0256 AC: 0.0256343 AN: 0.0256343

Gnomad4 ASJ AF: 0.0228 AC: 0.0227797 AN: 0.0227797

Gnomad4 EAS AF: 0.00251 AC: 0.00250675 AN: 0.00250675

Gnomad4 SAS AF: 0.00331 AC: 0.00331263 AN: 0.00331263

Gnomad4 FIN AF: 0.00160 AC: 0.00159985 AN: 0.00159985

Gnomad4 NFE AF: 0.0147 AC: 0.0146882 AN: 0.0146882

Gnomad4 OTH AF: 0.0303 AC: 0.0303318 AN: 0.0303318

Alfa AF: 0.0153 Hom.: 102

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

Jun 01, 1999

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

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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;