rs11022428

Variant names:

• chr11-12594663-C-T
• rs11022428

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 0.108 in 151,630 control chromosomes in the GnomAD database, including 1,011 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 0.11 (1011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 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: 0.108 AC: 16347 AN: 151512 Hom.: 1010 Cov.: 32

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.00407

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.108 AC: 16356 AN: 151630 Hom.: 1011 Cov.: 32 AF XY: 0.109 AC XY: 8043 AN XY: 74058

African (AFR) AF: 0.0494 AC: 2043 AN: 41384

American (AMR) AF: 0.170 AC: 2590 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3462

East Asian (EAS) AF: 0.00408 AC: 21 AN: 5144

South Asian (SAS) AF: 0.149 AC: 715 AN: 4792

European-Finnish (FIN) AF: 0.122 AC: 1268 AN: 10432

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.132 AC: 8937 AN: 67874

Other (OTH) AF: 0.133 AC: 280 AN: 2098

Alfa AF: 0.133 Hom.: 2287

Bravo AF: 0.108

Asia WGS AF: 0.0720 AC: 250 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.67
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11022428; hg19: chr11-12616210;