20-6393523-G-T

Variant names:

• chr20-6393523-G-T
• rs355530

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 0.763 in 152,192 control chromosomes in the GnomAD database, including 45,058 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 0.76 (45058 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 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: 0.763 AC: 116007 AN: 152074 Hom.: 45001 Cov.: 33

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.763 AC: 116123 AN: 152192 Hom.: 45058 Cov.: 33 AF XY: 0.763 AC XY: 56765 AN XY: 74398

African (AFR) AF: 0.896 AC: 37225 AN: 41532

American (AMR) AF: 0.755 AC: 11541 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2616 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4597 AN: 5178

South Asian (SAS) AF: 0.707 AC: 3407 AN: 4820

European-Finnish (FIN) AF: 0.730 AC: 7733 AN: 10586

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46614 AN: 67996

Other (OTH) AF: 0.776 AC: 1641 AN: 2116

Alfa AF: 0.715 Hom.: 61071

Bravo AF: 0.776

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.28
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs355530; hg19: chr20-6374170;