rs6051841

Positions:

• chr20-3412224-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 0.197 in 152,244 control chromosomes in the GnomAD database, including 3,260 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 (3260 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.04

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 (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.197 AC: 30002 AN: 152126 Hom.: 3256 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.197 AC: 30007 AN: 152244 Hom.: 3260 Cov.: 33 AF XY: 0.192 AC XY: 14319 AN XY: 74444

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.199

Alfa AF: 0.187 Hom.: 1215

Bravo AF: 0.206

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6051841; hg19: chr20-3392871;