rs11227306

Variant names:

• chr11-65811201-C-A
• rs11227306
• XM_047427980.1:c.*1058-7737G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047427980.1(LOC124902693):​c.*1058-7737G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,828 control chromosomes in the GnomAD database, including 7,924 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 0.31 (7924 hom., cov: 32)
• Consequence: LOC124902693 XM_047427980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 21 publications found

Genes affected

LOC124902693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47680 AN: 151710 Hom.: 7907 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.314 AC: 47730 AN: 151828 Hom.: 7924 Cov.: 32 AF XY: 0.305 AC XY: 22661 AN XY: 74234

African (AFR) AF: 0.267 AC: 11015 AN: 41254

American (AMR) AF: 0.281 AC: 4296 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3470

East Asian (EAS) AF: 0.300 AC: 1550 AN: 5164

South Asian (SAS) AF: 0.131 AC: 632 AN: 4814

European-Finnish (FIN) AF: 0.274 AC: 2905 AN: 10586

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25094 AN: 67962

Other (OTH) AF: 0.320 AC: 675 AN: 2108

Alfa AF: 0.349 Hom.: 20828

Bravo AF: 0.317

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs11227306; hg19: chr11-65578672;