20-4463514-A-G

Variant names:

• chr20-4463514-A-G
• rs6084754

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 0.385 in 152,116 control chromosomes in the GnomAD database, including 12,550 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 0.39 (12550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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: 0.385 AC: 58580 AN: 151998 Hom.: 12552 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.385 AC: 58578 AN: 152116 Hom.: 12550 Cov.: 32 AF XY: 0.385 AC XY: 28667 AN XY: 74368

African (AFR) AF: 0.195 AC: 8102 AN: 41498

American (AMR) AF: 0.339 AC: 5188 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3472

East Asian (EAS) AF: 0.582 AC: 3013 AN: 5178

South Asian (SAS) AF: 0.458 AC: 2206 AN: 4814

European-Finnish (FIN) AF: 0.486 AC: 5129 AN: 10560

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32287 AN: 67986

Other (OTH) AF: 0.398 AC: 841 AN: 2112

Alfa AF: 0.431 Hom.: 19199

Bravo AF: 0.364

Asia WGS AF: 0.485 AC: 1684 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.4
DANN	Benign	0.71
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6084754; hg19: chr20-4444161;