rs11115322

Variant names:

• chr12-82625409-T-C
• rs11115322
• XR_001749145.1:n.225-1104T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001749145.1(LOC107984487):​n.225-1104T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,226 control chromosomes in the GnomAD database, including 676 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 0.072 (676 hom., cov: 32)
• Consequence: LOC107984487 XR_001749145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

LOC107984487 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984487	XR_001749145.1	n.225-1104T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0713 AC: 10851 AN: 152108 Hom.: 668 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0225

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0716 AC: 10899 AN: 152226 Hom.: 676 Cov.: 32 AF XY: 0.0726 AC XY: 5405 AN XY: 74454

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.0755

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.0684

Gnomad4 FIN AF: 0.0202

Gnomad4 NFE AF: 0.0225

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0306 Hom.: 258

Bravo AF: 0.0783

Asia WGS AF: 0.116 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.61
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11115322; hg19: chr12-83019188;