rs11212364

Variant names:

• chr11-97703984-A-G
• rs11212364

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 0.0452 in 151,828 control chromosomes in the GnomAD database, including 289 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 0.045 (289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0882 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: 0.0452 AC: 6854 AN: 151710 Hom.: 288 Cov.: 32

Gnomad AFR AF: 0.00978

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.0959

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0467

Gnomad OTH AF: 0.0418

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

GnomAD4 genome AF: 0.0452 AC: 6868 AN: 151828 Hom.: 289 Cov.: 32 AF XY: 0.0485 AC XY: 3599 AN XY: 74214

African (AFR) AF: 0.00978 AC: 406 AN: 41516

American (AMR) AF: 0.0830 AC: 1260 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3468

East Asian (EAS) AF: 0.0951 AC: 490 AN: 5150

South Asian (SAS) AF: 0.0269 AC: 130 AN: 4824

European-Finnish (FIN) AF: 0.118 AC: 1250 AN: 10582

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0467 AC: 3169 AN: 67808

Other (OTH) AF: 0.0457 AC: 96 AN: 2102

Alfa AF: 0.0448 Hom.: 474

Bravo AF: 0.0433

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.79
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs11212364; hg19: chr11-97574984;