5-4488132-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901169	XR_007059108.1	n.2426G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248973	ENST00000507435.1	n.533-6377G>A		intron_variant	Intron 4 of 5	5
ENSG00000248973	ENST00000743499.1	n.549-6377G>A		intron_variant	Intron 2 of 4
ENSG00000248973	ENST00000743500.1	n.273-6377G>A		intron_variant	Intron 2 of 3

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 v4.3

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;