rs9509139

Variant names:

• chr13-20324177-T-C
• rs9509139
• XR_941720.2:n.201-1188T>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.201-1188T>C 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 151,802 control chromosomes in the GnomAD database, including 13,330 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 (13330 hom., cov: 31)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 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: 0.386 AC: 58575 AN: 151682 Hom.: 13324 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.515

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: 58597 AN: 151802 Hom.: 13330 Cov.: 31 AF XY: 0.384 AC XY: 28479 AN XY: 74168

African (AFR) AF: 0.140 AC: 5795 AN: 41424

American (AMR) AF: 0.430 AC: 6570 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1201 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1268 AN: 5142

South Asian (SAS) AF: 0.440 AC: 2116 AN: 4806

European-Finnish (FIN) AF: 0.494 AC: 5208 AN: 10540

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

European-Non Finnish (NFE) AF: 0.515 AC: 34950 AN: 67858

Other (OTH) AF: 0.399 AC: 838 AN: 2100

Alfa AF: 0.441 Hom.: 2025

Bravo AF: 0.369

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	-0.87
CADD	Benign	5.7
DANN	Benign	0.83
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9509139; hg19: chr13-20898316;