XR_001742829.2:n.201+18293G>T

Variant names:

• chr5-101612841-C-A
• rs13188771
• XR_001742829.2:n.201+18293G>T

Variant summary

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

The XR_001742829.2(LOC105379102):​n.201+18293G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,180 control chromosomes in the GnomAD database, including 1,783 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 (1783 hom., cov: 31)
• Consequence: LOC105379102 XR_001742829.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 7 publications found

Genes affected

LOC105379102 (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 (AMR) allele frequency at 95% confidence interval = 0.25 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: 0.135 AC: 20545 AN: 152062 Hom.: 1770 Cov.: 31

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.135 AC: 20571 AN: 152180 Hom.: 1783 Cov.: 31 AF XY: 0.137 AC XY: 10174 AN XY: 74400

African (AFR) AF: 0.0323 AC: 1340 AN: 41520

American (AMR) AF: 0.256 AC: 3919 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 779 AN: 3466

East Asian (EAS) AF: 0.217 AC: 1120 AN: 5170

South Asian (SAS) AF: 0.157 AC: 755 AN: 4822

European-Finnish (FIN) AF: 0.125 AC: 1322 AN: 10598

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10755 AN: 67996

Other (OTH) AF: 0.172 AC: 362 AN: 2110

Alfa AF: 0.153 Hom.: 5567

Bravo AF: 0.140

Asia WGS AF: 0.195 AC: 678 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	3.7
DANN	Benign	0.28
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs13188771; hg19: chr5-100948545;