rs4809696

Variant names:

• chr20-48445065-T-C
• rs4809696

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 0.331 in 151,992 control chromosomes in the GnomAD database, including 8,974 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 0.33 (8974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 2 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 (AMR) allele frequency at 95% confidence interval = 0.473 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: 0.330 AC: 50188 AN: 151872 Hom.: 8958 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.331 AC: 50239 AN: 151992 Hom.: 8974 Cov.: 32 AF XY: 0.333 AC XY: 24748 AN XY: 74308

African (AFR) AF: 0.223 AC: 9238 AN: 41466

American (AMR) AF: 0.483 AC: 7363 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3468

East Asian (EAS) AF: 0.477 AC: 2458 AN: 5154

South Asian (SAS) AF: 0.331 AC: 1592 AN: 4814

European-Finnish (FIN) AF: 0.326 AC: 3437 AN: 10552

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24137 AN: 67964

Other (OTH) AF: 0.339 AC: 715 AN: 2110

Alfa AF: 0.345 Hom.: 1919

Bravo AF: 0.342

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.79
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4809696; hg19: chr20-47073807;