rs3827143

Variant names:

• chr20-23638980-A-G
• rs3827143

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 0.203 in 152,136 control chromosomes in the GnomAD database, including 3,324 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 (3324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

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: 0.203 AC: 30834 AN: 152018 Hom.: 3324 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.189

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.203 AC: 30842 AN: 152136 Hom.: 3324 Cov.: 32 AF XY: 0.204 AC XY: 15141 AN XY: 74380

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.186

Alfa AF: 0.201 Hom.: 3991

Bravo AF: 0.190

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
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: rs3827143; hg19: chr20-23619617;