rs6123569

Variant names:

• chr20-56252715-T-A
• rs6123569

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 0.078 in 152,162 control chromosomes in the GnomAD database, including 591 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 0.078 (591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11851 AN: 152044 Hom.: 593 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.0337

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0631

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

GnomAD4 genome AF: 0.0780 AC: 11866 AN: 152162 Hom.: 591 Cov.: 32 AF XY: 0.0815 AC XY: 6063 AN XY: 74400

African (AFR) AF: 0.134 AC: 5541 AN: 41472

American (AMR) AF: 0.108 AC: 1648 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 277 AN: 3472

East Asian (EAS) AF: 0.0338 AC: 175 AN: 5180

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4820

European-Finnish (FIN) AF: 0.110 AC: 1168 AN: 10592

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0379 AC: 2579 AN: 68010

Other (OTH) AF: 0.0624 AC: 132 AN: 2114

Alfa AF: 0.0606 Hom.: 46

Bravo AF: 0.0764

Asia WGS AF: 0.0750 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.7
DANN	Benign	0.87
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs6123569; hg19: chr20-54827771;