XR_001740585.2:n.189-759G>A

Variant names:

• chr3-956829-G-A
• rs11131168
• XR_001740585.2:n.189-759G>A

Variant summary

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

The XR_001740585.2(LOC107986059):​n.189-759G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,856 control chromosomes in the GnomAD database, including 12,055 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 (12055 hom., cov: 32)
• Consequence: LOC107986059 XR_001740585.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 0 publications found

Genes affected

LOC107986059 (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 = 0.631 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: 0.389 AC: 59064 AN: 151736 Hom.: 12047 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.389 AC: 59099 AN: 151856 Hom.: 12055 Cov.: 32 AF XY: 0.392 AC XY: 29076 AN XY: 74204

African (AFR) AF: 0.330 AC: 13671 AN: 41406

American (AMR) AF: 0.479 AC: 7312 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1226 AN: 3462

East Asian (EAS) AF: 0.650 AC: 3322 AN: 5114

South Asian (SAS) AF: 0.608 AC: 2926 AN: 4812

European-Finnish (FIN) AF: 0.311 AC: 3281 AN: 10540

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26210 AN: 67946

Other (OTH) AF: 0.403 AC: 851 AN: 2114

Alfa AF: 0.392 Hom.: 52584

Bravo AF: 0.398

Asia WGS AF: 0.630 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11131168; hg19: chr3-998513;