XR_007060527.1:n.178+15465G>A

Variant names:

• chr7-130753455-G-A
• rs13234407
• XR_007060527.1:n.178+15465G>A

Variant summary

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

The XR_007060527.1(LOC105375508):​n.178+15465G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,054 control chromosomes in the GnomAD database, including 12,984 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 0.40 (12984 hom., cov: 31)
• Consequence: LOC105375508 XR_007060527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556
• Publications: 12 publications found

Genes affected

LOC105375508 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60908 AN: 151936 Hom.: 12979 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.401 AC: 60925 AN: 152054 Hom.: 12984 Cov.: 31 AF XY: 0.397 AC XY: 29531 AN XY: 74342

African (AFR) AF: 0.268 AC: 11121 AN: 41468

American (AMR) AF: 0.388 AC: 5929 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1324 AN: 3470

East Asian (EAS) AF: 0.307 AC: 1584 AN: 5166

South Asian (SAS) AF: 0.386 AC: 1858 AN: 4814

European-Finnish (FIN) AF: 0.450 AC: 4754 AN: 10566

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33115 AN: 67964

Other (OTH) AF: 0.421 AC: 890 AN: 2114

Alfa AF: 0.455 Hom.: 64312

Bravo AF: 0.389

Asia WGS AF: 0.376 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs13234407; hg19: chr7-130438214;