rs12873647

Variant names:

• chr13-20324140-G-A
• rs12873647
• XR_941720.2:n.201-1225G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-20324140-G-A
• chr13-20324140-G-C

Variant summary

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

The XR_941720.2(LOC105370102):​n.201-1225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,934 control chromosomes in the GnomAD database, including 13,374 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 0.39 (13374 hom., cov: 31)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 0 publications found

Genes affected

LOC105370102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 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: 0.386 AC: 58656 AN: 151816 Hom.: 13369 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.386 AC: 58676 AN: 151934 Hom.: 13374 Cov.: 31 AF XY: 0.384 AC XY: 28512 AN XY: 74232

African (AFR) AF: 0.140 AC: 5783 AN: 41448

American (AMR) AF: 0.431 AC: 6573 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1273 AN: 5146

South Asian (SAS) AF: 0.440 AC: 2115 AN: 4810

European-Finnish (FIN) AF: 0.494 AC: 5208 AN: 10546

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35036 AN: 67944

Other (OTH) AF: 0.399 AC: 842 AN: 2108

Alfa AF: 0.441 Hom.: 2032

Bravo AF: 0.368

Asia WGS AF: 0.395 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.55
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs12873647; hg19: chr13-20898279;