chr11-67592793-G-T

Variant names:

• chr11-67592793-G-T
• rs11227844

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 0.0524 in 152,244 control chromosomes in the GnomAD database, including 319 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 0.052 (319 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0748 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: 0.0525 AC: 7986 AN: 152126 Hom.: 319 Cov.: 33

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0454

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0882

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0524 AC: 7984 AN: 152244 Hom.: 319 Cov.: 33 AF XY: 0.0528 AC XY: 3930 AN XY: 74436

African (AFR) AF: 0.0133 AC: 552 AN: 41554

American (AMR) AF: 0.0453 AC: 693 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0126 AC: 61 AN: 4830

European-Finnish (FIN) AF: 0.0882 AC: 934 AN: 10584

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0766 AC: 5207 AN: 68012

Other (OTH) AF: 0.0526 AC: 111 AN: 2112

Alfa AF: 0.0692 Hom.: 869

Bravo AF: 0.0484

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.96
DANN	Benign	0.92
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11227844; hg19: chr11-67360264;