XR_001749145.1:n.225-1104T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

LOC107984487 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.157 AC: 6529 AN: 41518

American (AMR) AF: 0.0755 AC: 1154 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3466

East Asian (EAS) AF: 0.170 AC: 880 AN: 5184

South Asian (SAS) AF: 0.0684 AC: 330 AN: 4824

European-Finnish (FIN) AF: 0.0202 AC: 214 AN: 10612

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0225 AC: 1530 AN: 68020

Other (OTH) AF: 0.0629 AC: 133 AN: 2116

Alfa AF: 0.0381 Hom.: 897

Bravo AF: 0.0783

Asia WGS AF: 0.116 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.61
DANN	Benign	0.59
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11115322; hg19: chr12-83019188;