rs4803223

chr19-39255579-A-Gchr19-39255579-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;