rs45461302

Positions:

• chr20-45176633-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 0.156 in 159,910 control chromosomes in the GnomAD database, including 2,073 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 0.16 (1986 hom., cov: 32)
  • Exomes 𝑓: 0.13 (87 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 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: 0.157 AC: 23816 AN: 151948 Hom.: 1981 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0328

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.131 AC: 1030 AN: 7844 Hom.: 87 AF XY: 0.133 AC XY: 557 AN XY: 4194

Gnomad4 AFR exome AF: 0.0698

Gnomad4 AMR exome AF: 0.0921

Gnomad4 ASJ exome AF: 0.0909

Gnomad4 EAS exome AF: 0.0232

Gnomad4 SAS exome AF: 0.135

Gnomad4 FIN exome AF: 0.154

Gnomad4 NFE exome AF: 0.151

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.157 AC: 23855 AN: 152066 Hom.: 1986 Cov.: 32 AF XY: 0.157 AC XY: 11677 AN XY: 74312

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0326

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.166

Alfa AF: 0.170 Hom.: 282

Bravo AF: 0.151

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45461302; hg19: chr20-43805274;