20-5219581-C-T

Variant names:

• chr20-5219581-C-T
• rs6107598

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 0.314 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.219 AC: 9077 AN: 41438

American (AMR) AF: 0.309 AC: 4721 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1207 AN: 3472

East Asian (EAS) AF: 0.132 AC: 682 AN: 5168

South Asian (SAS) AF: 0.377 AC: 1815 AN: 4820

European-Finnish (FIN) AF: 0.331 AC: 3489 AN: 10548

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.379 AC: 25777 AN: 67940

Other (OTH) AF: 0.309 AC: 653 AN: 2112

Alfa AF: 0.350 Hom.: 11635

Bravo AF: 0.305

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	13
DANN	Benign	0.93
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs6107598; hg19: chr20-5200227;