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. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0785 AC: 3186 AN: 40604

American (AMR) AF: 0.254 AC: 3849 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 595 AN: 3454

East Asian (EAS) AF: 0.0827 AC: 427 AN: 5166

South Asian (SAS) AF: 0.153 AC: 734 AN: 4796

European-Finnish (FIN) AF: 0.0720 AC: 755 AN: 10488

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9929 AN: 67874

Other (OTH) AF: 0.162 AC: 339 AN: 2090

Alfa AF: 0.146 Hom.: 4223

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4803223; hg19: chr19-39746219;