rs1520173

Variant names:

• chr12-115744720-A-G
• rs1520173
• XR_945388.3:n.118+18228T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-115744720-A-G
• chr12-115744720-A-T

Variant summary

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

The XR_945388.3(LOC105370003):​n.118+18228T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,844 control chromosomes in the GnomAD database, including 4,710 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 0.23 (4710 hom., cov: 31)
• Consequence: LOC105370003 XR_945388.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.774
• Publications: 2 publications found

Genes affected

LOC105370003 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 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: 0.226 AC: 34253 AN: 151726 Hom.: 4700 Cov.: 31

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.226 AC: 34289 AN: 151844 Hom.: 4710 Cov.: 31 AF XY: 0.233 AC XY: 17261 AN XY: 74180

African (AFR) AF: 0.164 AC: 6801 AN: 41404

American (AMR) AF: 0.398 AC: 6063 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2867 AN: 5102

South Asian (SAS) AF: 0.372 AC: 1787 AN: 4800

European-Finnish (FIN) AF: 0.164 AC: 1728 AN: 10530

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13277 AN: 67990

Other (OTH) AF: 0.270 AC: 571 AN: 2114

Alfa AF: 0.214 Hom.: 6253

Bravo AF: 0.241

Asia WGS AF: 0.471 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.4
DANN	Benign	0.78
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs1520173; hg19: chr12-116182525;