XR_941985.2:n.114+12534A>G

Variant names:

• chr13-58672160-T-C
• rs9569918
• XR_941985.2:n.114+12534A>G

Variant summary

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

The XR_941985.2(LOC105370219):​n.114+12534A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,026 control chromosomes in the GnomAD database, including 3,285 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 0.19 (3285 hom., cov: 32)
• Consequence: LOC105370219 XR_941985.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 6 publications found

Genes affected

LOC105370219 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 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: 0.190 AC: 28859 AN: 151908 Hom.: 3278 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.190 AC: 28878 AN: 152026 Hom.: 3285 Cov.: 32 AF XY: 0.195 AC XY: 14478 AN XY: 74304

African (AFR) AF: 0.114 AC: 4717 AN: 41516

American (AMR) AF: 0.227 AC: 3469 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3468

East Asian (EAS) AF: 0.499 AC: 2577 AN: 5160

South Asian (SAS) AF: 0.376 AC: 1814 AN: 4820

European-Finnish (FIN) AF: 0.168 AC: 1771 AN: 10564

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13414 AN: 67932

Other (OTH) AF: 0.201 AC: 423 AN: 2108

Alfa AF: 0.188 Hom.: 516

Bravo AF: 0.188

Asia WGS AF: 0.389 AC: 1339 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.78
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9569918; hg19: chr13-59246294;