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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370003	XR_945388.3	n.118+18228T>C		intron_variant	Intron 1 of 3
LOC105370003	XR_945389.3	n.118+18228T>C		intron_variant	Intron 1 of 3

Ensembl

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

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 v4.3

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;