rs1216592

Variant names:

• chr11-100576727-T-G
• rs1216592

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 0.328 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.420 AC: 17426 AN: 41466

American (AMR) AF: 0.271 AC: 4143 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 876 AN: 3472

East Asian (EAS) AF: 0.122 AC: 632 AN: 5184

South Asian (SAS) AF: 0.212 AC: 1022 AN: 4824

European-Finnish (FIN) AF: 0.248 AC: 2628 AN: 10590

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 22069 AN: 67984

Other (OTH) AF: 0.326 AC: 687 AN: 2108

Alfa AF: 0.330 Hom.: 10050

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
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs1216592; hg19: chr11-100447458;