chr4-38334253-T-G

Variant names:

• chr4-38334253-T-G
• rs10517478
• ENST00000503465.2:n.235-32618T>G

Variant summary

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

The ENST00000503465.2(LINC02513):​n.235-32618T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 152,270 control chromosomes in the GnomAD database, including 715 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 0.046 (715 hom., cov: 32)
• Consequence: LINC02513 ENST00000503465.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 1 publications found

Genes affected

LINC02513 (HGNC:53502): (long intergenic non-protein coding RNA 2513)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503465.2. You can select a different transcript below to see updated ACMG assignments.

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
	LINC02513	ENST00000503465.2	TSL:2	n.235-32618T>G		intron	N/A
	LINC02513	ENST00000757609.1		n.235-32618T>G		intron	N/A
	LINC02513	ENST00000757610.1		n.216-32618T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 6981 AN: 152152 Hom.: 720 Cov.: 32

Gnomad AFR AF: 0.00992

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.00951

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.0668

Gnomad FIN AF: 0.0325

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0245

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0458 AC: 6970 AN: 152270 Hom.: 715 Cov.: 32 AF XY: 0.0502 AC XY: 3739 AN XY: 74446

African (AFR) AF: 0.00989 AC: 411 AN: 41568

American (AMR) AF: 0.114 AC: 1738 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00951 AC: 33 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2346 AN: 5178

South Asian (SAS) AF: 0.0660 AC: 318 AN: 4816

European-Finnish (FIN) AF: 0.0325 AC: 345 AN: 10624

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0245 AC: 1663 AN: 68002

Other (OTH) AF: 0.0445 AC: 94 AN: 2112

Alfa AF: 0.0169 Hom.: 6

Bravo AF: 0.0543

Asia WGS AF: 0.204 AC: 707 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.66
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10517478; hg19: chr4-38335874;