rs6598020

Variant names:

• chr11-444628-C-T
• rs6598020

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.335 AC: 13900 AN: 41526

American (AMR) AF: 0.167 AC: 2557 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3472

East Asian (EAS) AF: 0.180 AC: 932 AN: 5178

South Asian (SAS) AF: 0.200 AC: 968 AN: 4834

European-Finnish (FIN) AF: 0.189 AC: 2007 AN: 10598

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12493 AN: 68018

Other (OTH) AF: 0.224 AC: 473 AN: 2112

Alfa AF: 0.193 Hom.: 3612

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6598020; hg19: chr11-444628;