rs2267864

chr20-45176638-C-Gchr20-45176638-C-T

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 0.199 in 158,766 control chromosomes in the GnomAD database, including 3,232 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 0.20 (3115 hom., cov: 32)
  • Exomes 𝑓: 0.16 (117 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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: 0.201 AC: 30476 AN: 151766 Hom.: 3102 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.204

GnomAD4 exome AF: 0.163 AC: 1122 AN: 6882 Hom.: 117 AF XY: 0.168 AC XY: 621 AN XY: 3692

Gnomad4 AFR exome AF: 0.182

Gnomad4 AMR exome AF: 0.160

Gnomad4 ASJ exome AF: 0.0909

Gnomad4 EAS exome AF: 0.103

Gnomad4 SAS exome AF: 0.160

Gnomad4 FIN exome AF: 0.200

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.162

GnomAD4 genome AF: 0.201 AC: 30540 AN: 151884 Hom.: 3115 Cov.: 32 AF XY: 0.204 AC XY: 15110 AN XY: 74216

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.207

Alfa AF: 0.0981 Hom.: 137

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.5
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2267864; hg19: chr20-43805279;