rs7578117

Variant names:

• chr2-38462479-G-C
• rs7578117
• ENST00000413227.2:n.1157+424C>G

Variant summary

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

The ENST00000413227.2(LINC02613):​n.1157+424C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0606 in 152,270 control chromosomes in the GnomAD database, including 782 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 0.061 (782 hom., cov: 32)
• Consequence: LINC02613 ENST00000413227.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.706
• Publications: 0 publications found

Genes affected

LINC02613 (HGNC:54068): (long intergenic non-protein coding RNA 2613)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413227.2. 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
	LINC02613	NR_110259.1		n.895-3604C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02613	ENST00000413227.2	TSL:2	n.1157+424C>G		intron	N/A
	LINC02613	ENST00000417039.6	TSL:5	n.894+6765C>G		intron	N/A
	LINC02613	ENST00000421463.6	TSL:3	n.879-3604C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0605 AC: 9198 AN: 152152 Hom.: 779 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00800

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0606 AC: 9220 AN: 152270 Hom.: 782 Cov.: 32 AF XY: 0.0588 AC XY: 4381 AN XY: 74460

African (AFR) AF: 0.196 AC: 8117 AN: 41518

American (AMR) AF: 0.0228 AC: 349 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4832

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10620

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00800 AC: 544 AN: 68030

Other (OTH) AF: 0.0393 AC: 83 AN: 2112

Alfa AF: 0.0390 Hom.: 60

Bravo AF: 0.0673

Asia WGS AF: 0.0140 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	14
DANN	Benign	0.73
PhyloP100		0.71
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7578117; hg19: chr2-38689621;