rs4810479

Variant names:

• chr20-45916409-C-T
• rs4810479

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 0.671 in 152,116 control chromosomes in the GnomAD database, including 35,050 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 0.67 (35050 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 70 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 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: 0.672 AC: 102080 AN: 151998 Hom.: 35044 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.671 AC: 102103 AN: 152116 Hom.: 35050 Cov.: 33 AF XY: 0.664 AC XY: 49393 AN XY: 74344

African (AFR) AF: 0.603 AC: 25019 AN: 41492

American (AMR) AF: 0.595 AC: 9094 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2532 AN: 3472

East Asian (EAS) AF: 0.384 AC: 1984 AN: 5164

South Asian (SAS) AF: 0.525 AC: 2534 AN: 4824

European-Finnish (FIN) AF: 0.731 AC: 7733 AN: 10582

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50830 AN: 67980

Other (OTH) AF: 0.674 AC: 1423 AN: 2110

Alfa AF: 0.718 Hom.: 169052

Bravo AF: 0.655

Asia WGS AF: 0.408 AC: 1425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4810479; hg19: chr20-44545048;