XR_007064320.1:n.539-600A>G

Variant names:

• chr14-95702794-A-G
• rs7158782
• XR_007064320.1:n.539-600A>G

Variant summary

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

The XR_007064320.1(LOC124903373):​n.539-600A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,818 control chromosomes in the GnomAD database, including 11,351 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 0.31 (11351 hom., cov: 32)
• Consequence: LOC124903373 XR_007064320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• Publications: 19 publications found

Genes affected

LOC124903373 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46352 AN: 151700 Hom.: 11313 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.306 AC: 46449 AN: 151818 Hom.: 11351 Cov.: 32 AF XY: 0.306 AC XY: 22720 AN XY: 74250

African (AFR) AF: 0.683 AC: 28162 AN: 41244

American (AMR) AF: 0.217 AC: 3317 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1144 AN: 5164

South Asian (SAS) AF: 0.218 AC: 1046 AN: 4806

European-Finnish (FIN) AF: 0.224 AC: 2368 AN: 10556

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9165 AN: 67976

Other (OTH) AF: 0.245 AC: 517 AN: 2110

Alfa AF: 0.186 Hom.: 17949

Bravo AF: 0.320

Asia WGS AF: 0.263 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.54
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7158782; hg19: chr14-96169131;