rs12300899

Variant names:

• chr12-125062029-C-T
• rs12300899
• XR_001749365.2:n.303-720G>A

Variant summary

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

The XR_001749365.2(LOC105370052):​n.303-720G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 137,538 control chromosomes in the GnomAD database, including 1,542 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 0.14 (1542 hom., cov: 30)
• Consequence: LOC105370052 XR_001749365.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 1 publications found

Genes affected

LOC105370052 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 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: 0.139 AC: 19155 AN: 137494 Hom.: 1538 Cov.: 30

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.139 AC: 19170 AN: 137538 Hom.: 1542 Cov.: 30 AF XY: 0.148 AC XY: 9835 AN XY: 66358

African (AFR) AF: 0.0728 AC: 2706 AN: 37156

American (AMR) AF: 0.207 AC: 2867 AN: 13830

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 557 AN: 3242

East Asian (EAS) AF: 0.245 AC: 1139 AN: 4656

South Asian (SAS) AF: 0.163 AC: 708 AN: 4350

European-Finnish (FIN) AF: 0.313 AC: 2608 AN: 8336

Middle Eastern (MID) AF: 0.117 AC: 31 AN: 266

European-Non Finnish (NFE) AF: 0.130 AC: 8184 AN: 63010

Other (OTH) AF: 0.149 AC: 275 AN: 1850

Alfa AF: 0.0180 Hom.: 14

Bravo AF: 0.125

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.79
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs12300899; hg19: chr12-125546575;