rs2231829

chr20-45547937-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 0.0233 in 653,586 control chromosomes in the GnomAD database, including 362 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 0.035 (166 hom., cov: 31)
  • Exomes 𝑓: 0.020 (196 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

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 (EAS) allele frequency at 95% confidence interval = 0.157 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: 0.0349 AC: 5291 AN: 151640 Hom.: 168 Cov.: 31

Gnomad AFR AF: 0.0401

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0159

Gnomad OTH AF: 0.0341

GnomAD4 exome AF: 0.0198 AC: 9917 AN: 501828 Hom.: 196 AF XY: 0.0197 AC XY: 4653 AN XY: 235768

Gnomad4 AFR exome AF: 0.0442

Gnomad4 AMR exome AF: 0.0365

Gnomad4 ASJ exome AF: 0.00962

Gnomad4 EAS exome AF: 0.162

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.00549

Gnomad4 NFE exome AF: 0.0159

Gnomad4 OTH exome AF: 0.0370

GnomAD4 genome AF: 0.0349 AC: 5298 AN: 151758 Hom.: 166 Cov.: 31 AF XY: 0.0380 AC XY: 2819 AN XY: 74154

Gnomad4 AFR AF: 0.0403

Gnomad4 AMR AF: 0.0496

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0289

Gnomad4 NFE AF: 0.0159

Gnomad4 OTH AF: 0.0343

Alfa AF: 0.0254 Hom.: 13

Bravo AF: 0.0357

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.98
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2231829; hg19: chr20-44176576;