chr5-34525826-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900958	XR_007058727.1	n.-130A>G		upstream_gene_variant

Ensembl

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

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 v4.3

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;