rs6598020

chr11-444628-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 0.225 in 152,230 control chromosomes in the GnomAD database, including 4,280 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 0.23 (4280 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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 (AFR) allele frequency at 95% confidence interval = 0.33 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: 0.225 AC: 34292 AN: 152112 Hom.: 4271 Cov.: 33

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.225 AC: 34316 AN: 152230 Hom.: 4280 Cov.: 33 AF XY: 0.225 AC XY: 16738 AN XY: 74438

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.224

Alfa AF: 0.192 Hom.: 3073

Bravo AF: 0.226

Asia WGS AF: 0.212 AC: 735 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	0.077
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6598020; hg19: chr11-444628;