20-5219581-C-T

Variant names:

• chr20-5219581-C-T
• rs6107598

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 0.314 in 151,972 control chromosomes in the GnomAD database, including 8,014 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 0.31 (8014 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.926

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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: 0.315 AC: 47764 AN: 151856 Hom.: 8007 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.314 AC: 47782 AN: 151972 Hom.: 8014 Cov.: 31 AF XY: 0.312 AC XY: 23161 AN XY: 74274

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.309

Alfa AF: 0.356 Hom.: 9035

Bravo AF: 0.305

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	13
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6107598; hg19: chr20-5200227;