rs11574528

Variant names:

• chr22-43131675-C-T
• rs11574528

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 0.216 in 152,128 control chromosomes in the GnomAD database, including 4,323 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 0.22 (4323 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.956
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32842 AN: 152010 Hom.: 4312 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.216 AC: 32885 AN: 152128 Hom.: 4323 Cov.: 33 AF XY: 0.214 AC XY: 15951 AN XY: 74370

African (AFR) AF: 0.365 AC: 15150 AN: 41472

American (AMR) AF: 0.150 AC: 2296 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3472

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5170

South Asian (SAS) AF: 0.146 AC: 702 AN: 4824

European-Finnish (FIN) AF: 0.159 AC: 1684 AN: 10590

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11891 AN: 68002

Other (OTH) AF: 0.202 AC: 428 AN: 2114

Alfa AF: 0.185 Hom.: 4842

Bravo AF: 0.221

Asia WGS AF: 0.108 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.77
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs11574528; hg19: chr22-43527681;