XR_001750061.1:n.79-3514C>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370284	XR_001750061.1	n.79-3514C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;