20-56270740-G-A

Variant names:

• chr20-56270740-G-A
• rs6064362

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 0.505 in 152,026 control chromosomes in the GnomAD database, including 21,727 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 0.51 (21727 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76827 AN: 151908 Hom.: 21734 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.505 AC: 76838 AN: 152026 Hom.: 21727 Cov.: 33 AF XY: 0.502 AC XY: 37312 AN XY: 74296

African (AFR) AF: 0.257 AC: 10673 AN: 41478

American (AMR) AF: 0.503 AC: 7687 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1978 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1410 AN: 5186

South Asian (SAS) AF: 0.553 AC: 2661 AN: 4814

European-Finnish (FIN) AF: 0.605 AC: 6378 AN: 10534

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44031 AN: 67956

Other (OTH) AF: 0.542 AC: 1143 AN: 2110

Alfa AF: 0.598 Hom.: 117205

Bravo AF: 0.484

Asia WGS AF: 0.413 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.73
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs6064362; hg19: chr20-54845796;