rs1800625

Positions:

• chr6-32184665-A-G

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 0.147 in 207,222 control chromosomes in the GnomAD database, including 2,516 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.15 (1731 hom., cov: 33)
  • Exomes 𝑓: 0.15 (785 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32184665A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.146 AC: 21856 AN: 150010 Hom.: 1736 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.149 AC: 8525 AN: 57098 Hom.: 785 AF XY: 0.151 AC XY: 4320 AN XY: 28580

Gnomad4 AFR exome AF: 0.0998

Gnomad4 AMR exome AF: 0.0746

Gnomad4 ASJ exome AF: 0.0919

Gnomad4 EAS exome AF: 0.0931

Gnomad4 SAS exome AF: 0.147

Gnomad4 FIN exome AF: 0.128

Gnomad4 NFE exome AF: 0.169

Gnomad4 OTH exome AF: 0.151

GnomAD4 genome AF: 0.146 AC: 21846 AN: 150124 Hom.: 1731 Cov.: 33 AF XY: 0.141 AC XY: 10358 AN XY: 73390

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0824

Gnomad4 ASJ AF: 0.0876

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.129

Alfa AF: 0.162 Hom.: 193

Bravo AF: 0.140

Asia WGS AF: 0.113 AC: 392 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800625; hg19: chr6-32152442;