rs1216592

chr11-100576727-T-G

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 0.328 in 152,120 control chromosomes in the GnomAD database, including 8,688 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 0.33 (8688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.705

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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: 0.328 AC: 49848 AN: 152002 Hom.: 8670 Cov.: 33

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.328 AC: 49899 AN: 152120 Hom.: 8688 Cov.: 33 AF XY: 0.322 AC XY: 23980 AN XY: 74376

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.326

Alfa AF: 0.326 Hom.: 7702

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	12
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1216592; hg19: chr11-100447458;