5-34525826-A-G

Variant names:

• chr5-34525826-A-G
• rs10075914
• XR_007058727.1:n.-130A>G

Variant summary

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

The XR_007058727.1(LOC124900958):​n.-130A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,060 control chromosomes in the GnomAD database, including 34,910 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 0.67 (34910 hom., cov: 32)
• Consequence: LOC124900958 XR_007058727.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35
• Publications: 4 publications found

Genes affected

LOC124900958 (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 (EAS) allele frequency at 95% confidence interval = 0.898 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: 0.669 AC: 101605 AN: 151942 Hom.: 34896 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.669 AC: 101663 AN: 152060 Hom.: 34910 Cov.: 32 AF XY: 0.667 AC XY: 49605 AN XY: 74316

African (AFR) AF: 0.537 AC: 22242 AN: 41442

American (AMR) AF: 0.802 AC: 12256 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2534 AN: 3472

East Asian (EAS) AF: 0.920 AC: 4760 AN: 5174

South Asian (SAS) AF: 0.849 AC: 4098 AN: 4826

European-Finnish (FIN) AF: 0.559 AC: 5898 AN: 10554

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47605 AN: 67986

Other (OTH) AF: 0.729 AC: 1538 AN: 2110

Alfa AF: 0.702 Hom.: 126001

Bravo AF: 0.683

Asia WGS AF: 0.878 AC: 3050 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	0.67
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs10075914; hg19: chr5-34525931;