13-81839234-C-T

Variant names:

• chr13-81839234-C-T
• rs9545880
• XR_001750061.1:n.79-3514C>T

Variant summary

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

The XR_001750061.1(LOC105370284):​n.79-3514C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,980 control chromosomes in the GnomAD database, including 36,150 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 0.68 (36150 hom., cov: 32)
• Consequence: LOC105370284 XR_001750061.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 4 publications found

Genes affected

LOC105370284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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: 0.679 AC: 103155 AN: 151862 Hom.: 36136 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.679 AC: 103204 AN: 151980 Hom.: 36150 Cov.: 32 AF XY: 0.684 AC XY: 50842 AN XY: 74284

African (AFR) AF: 0.498 AC: 20627 AN: 41416

American (AMR) AF: 0.694 AC: 10596 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2597 AN: 3468

East Asian (EAS) AF: 0.912 AC: 4693 AN: 5148

South Asian (SAS) AF: 0.854 AC: 4119 AN: 4822

European-Finnish (FIN) AF: 0.774 AC: 8200 AN: 10590

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49915 AN: 67966

Other (OTH) AF: 0.712 AC: 1499 AN: 2106

Alfa AF: 0.690 Hom.: 6419

Bravo AF: 0.663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.27
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs9545880; hg19: chr13-82413369;