20-4563547-G-A

Variant names:

• chr20-4563547-G-A
• rs4141626

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 0.866 in 152,170 control chromosomes in the GnomAD database, including 57,683 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 0.87 (57683 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.927 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: 0.866 AC: 131650 AN: 152052 Hom.: 57672 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.866 AC: 131707 AN: 152170 Hom.: 57683 Cov.: 32 AF XY: 0.872 AC XY: 64832 AN XY: 74388

African (AFR) AF: 0.714 AC: 29630 AN: 41480

American (AMR) AF: 0.912 AC: 13944 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3047 AN: 3472

East Asian (EAS) AF: 0.888 AC: 4596 AN: 5174

South Asian (SAS) AF: 0.950 AC: 4577 AN: 4818

European-Finnish (FIN) AF: 0.985 AC: 10458 AN: 10612

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62530 AN: 67998

Other (OTH) AF: 0.870 AC: 1841 AN: 2116

Alfa AF: 0.895 Hom.: 23324

Bravo AF: 0.852

Asia WGS AF: 0.907 AC: 3152 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.6
DANN	Benign	0.80
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4141626; hg19: chr20-4544193;