rs11883223

Variant names:

• chr19-7657750-G-A
• rs11883223

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 0.227 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.247 AC: 10249 AN: 41496

American (AMR) AF: 0.328 AC: 5009 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2674 AN: 5182

South Asian (SAS) AF: 0.107 AC: 516 AN: 4826

European-Finnish (FIN) AF: 0.280 AC: 2956 AN: 10574

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12108 AN: 67986

Other (OTH) AF: 0.224 AC: 473 AN: 2112

Alfa AF: 0.199 Hom.: 13017

Bravo AF: 0.237

Asia WGS AF: 0.305 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.26
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs11883223; hg19: chr19-7722636;