rs4803223

Variant names:

• chr19-39255579-A-G
• rs4803223

Your query was ambiguous. Multiple possible variants found:

• chr19-39255579-A-G
• chr19-39255579-A-T

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 0.133 in 150,854 control chromosomes in the GnomAD database, including 1,632 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 0.13 (1632 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 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: 0.133 AC: 20003 AN: 150738 Hom.: 1634 Cov.: 31

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0827

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.133 AC: 20007 AN: 150854 Hom.: 1632 Cov.: 31 AF XY: 0.131 AC XY: 9654 AN XY: 73692

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0827

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0720

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.162

Alfa AF: 0.148 Hom.: 2394

Bravo AF: 0.146

Asia WGS AF: 0.103 AC: 359 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.0
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4803223; hg19: chr19-39746219;