XR_924392.3:n.283+17295C>T

Variant names:

• chr3-120163241-C-T
• rs13079094
• XR_924392.3:n.283+17295C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_924392.3(LOC105374065):​n.283+17295C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,000 control chromosomes in the GnomAD database, including 5,941 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 0.26 (5941 hom., cov: 31)
• Consequence: LOC105374065 XR_924392.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

Genes affected

LOC105374065 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374065	XR_924392.3	n.283+17295C>T		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40164 AN: 151884 Hom.: 5943 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.264 AC: 40174 AN: 152000 Hom.: 5941 Cov.: 31 AF XY: 0.264 AC XY: 19603 AN XY: 74302

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.259

Alfa AF: 0.295 Hom.: 4554

Bravo AF: 0.257

Asia WGS AF: 0.137 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.94
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13079094; hg19: chr3-119882088;