XR_007059108.1:n.2426G>A

Variant names:

• chr5-4488132-C-T
• rs10462794
• XR_007059108.1:n.2426G>A

Variant summary

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

The XR_007059108.1(LOC124901169):​n.2426G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,068 control chromosomes in the GnomAD database, including 40,812 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 0.73 (40812 hom., cov: 31)
• Consequence: LOC124901169 XR_007059108.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 2 publications found

Genes affected

LOC124901169 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507435.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000248973	ENST00000507435.1	TSL:5	n.533-6377G>A		intron	N/A
	ENSG00000248973	ENST00000743499.1		n.549-6377G>A		intron	N/A
	ENSG00000248973	ENST00000743500.1		n.273-6377G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110756 AN: 151950 Hom.: 40805 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.729 AC: 110793 AN: 152068 Hom.: 40812 Cov.: 31 AF XY: 0.725 AC XY: 53866 AN XY: 74318

African (AFR) AF: 0.657 AC: 27243 AN: 41462

American (AMR) AF: 0.693 AC: 10591 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2678 AN: 3470

East Asian (EAS) AF: 0.970 AC: 4997 AN: 5152

South Asian (SAS) AF: 0.645 AC: 3111 AN: 4820

European-Finnish (FIN) AF: 0.710 AC: 7508 AN: 10572

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.767 AC: 52174 AN: 67994

Other (OTH) AF: 0.746 AC: 1576 AN: 2114

Alfa AF: 0.742 Hom.: 18999

Bravo AF: 0.725

Asia WGS AF: 0.798 AC: 2778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.33
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs10462794; hg19: chr5-4488245;