12-115652459-C-T

Variant names:

• chr12-115652459-C-T
• rs7308283
• XR_945388.3:n.118+110489G>A

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+110489G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,822 control chromosomes in the GnomAD database, including 8,250 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 0.32 (8250 hom., cov: 30)
• Consequence: LOC105370003 XR_945388.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 3 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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: 0.321 AC: 48725 AN: 151704 Hom.: 8249 Cov.: 30

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.321 AC: 48740 AN: 151822 Hom.: 8250 Cov.: 30 AF XY: 0.322 AC XY: 23852 AN XY: 74158

African (AFR) AF: 0.246 AC: 10172 AN: 41400

American (AMR) AF: 0.229 AC: 3494 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1398 AN: 5134

South Asian (SAS) AF: 0.292 AC: 1399 AN: 4796

European-Finnish (FIN) AF: 0.461 AC: 4857 AN: 10526

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25169 AN: 67914

Other (OTH) AF: 0.323 AC: 683 AN: 2112

Alfa AF: 0.324 Hom.: 5142

Bravo AF: 0.301

Asia WGS AF: 0.290 AC: 1010 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.7
DANN	Benign	0.79
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs7308283; hg19: chr12-116090264;