rs4809696

Variant names:

• chr20-48445065-T-C
• rs4809696

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.339

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4809696; hg19: chr20-47073807;