XR_931637.2:n.693+126T>C

Variant names:

• chr13-90887481-T-C
• rs9523165
• XR_931637.2:n.693+126T>C

Variant summary

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

The XR_931637.2(LOC105370311):​n.693+126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,120 control chromosomes in the GnomAD database, including 7,819 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 0.30 (7819 hom., cov: 32)
• Consequence: LOC105370311 XR_931637.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 3 publications found

Genes affected

LOC105370311 (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 = 0.541 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: 0.300 AC: 45609 AN: 152002 Hom.: 7812 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.300 AC: 45622 AN: 152120 Hom.: 7819 Cov.: 32 AF XY: 0.306 AC XY: 22768 AN XY: 74368

African (AFR) AF: 0.145 AC: 6009 AN: 41528

American (AMR) AF: 0.433 AC: 6609 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1182 AN: 3472

East Asian (EAS) AF: 0.558 AC: 2886 AN: 5176

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4818

European-Finnish (FIN) AF: 0.341 AC: 3611 AN: 10576

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22095 AN: 67978

Other (OTH) AF: 0.297 AC: 624 AN: 2104

Alfa AF: 0.327 Hom.: 3791

Bravo AF: 0.301

Asia WGS AF: 0.435 AC: 1512 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.47
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs9523165; hg19: chr13-91539735;