20-6054582-C-T

Variant names:

• chr20-6054582-C-T
• rs2326679

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 0.771 in 151,866 control chromosomes in the GnomAD database, including 45,598 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 0.77 (45598 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 18 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 = 0.864 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: 0.771 AC: 117052 AN: 151750 Hom.: 45552 Cov.: 30

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.771 AC: 117157 AN: 151866 Hom.: 45598 Cov.: 30 AF XY: 0.768 AC XY: 57016 AN XY: 74202

African (AFR) AF: 0.872 AC: 36067 AN: 41360

American (AMR) AF: 0.791 AC: 12094 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2669 AN: 3468

East Asian (EAS) AF: 0.800 AC: 4139 AN: 5172

South Asian (SAS) AF: 0.783 AC: 3778 AN: 4822

European-Finnish (FIN) AF: 0.632 AC: 6626 AN: 10480

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49222 AN: 67964

Other (OTH) AF: 0.785 AC: 1654 AN: 2108

Alfa AF: 0.747 Hom.: 147594

Bravo AF: 0.786

Asia WGS AF: 0.817 AC: 2841 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	1.6
DANN	Benign	0.55
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs2326679; hg19: chr20-6035228;