rs11022428

chr11-12594663-C-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 0.108 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.00408

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.133

Alfa AF: 0.134 Hom.: 1823

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11022428; hg19: chr11-12616210;