rs11883223

Variant names:

• chr19-7657750-G-A
• rs11883223

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 0.227 in 152,116 control chromosomes in the GnomAD database, including 4,377 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 0.23 (4377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 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: 0.227 AC: 34533 AN: 151998 Hom.: 4359 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.227 AC: 34582 AN: 152116 Hom.: 4377 Cov.: 32 AF XY: 0.235 AC XY: 17473 AN XY: 74356

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.224

Alfa AF: 0.191 Hom.: 5207

Bravo AF: 0.237

Asia WGS AF: 0.305 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11883223; hg19: chr19-7722636;