rs1479211

Variant names:

• chr5-118230595-A-G
• rs1479211
• ENST00000509367.3:n.430-34759A>G

Variant summary

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

The ENST00000509367.3(LINC02147):​n.430-34759A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,972 control chromosomes in the GnomAD database, including 15,469 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 0.42 (15469 hom., cov: 31)
• Consequence: LINC02147 ENST00000509367.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 3 publications found

Genes affected

LINC02147 (HGNC:53007): (long intergenic non-protein coding RNA 2147)

LINC02208 (HGNC:52978): (long intergenic non-protein coding RNA 2208)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509367.3. 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
	LINC02147	NR_104997.1		n.171-34759A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02147	ENST00000509367.3	TSL:2	n.430-34759A>G		intron	N/A
	LINC02208	ENST00000660173.1		n.688-79134T>C		intron	N/A
	LINC02147	ENST00000661774.1		n.277-34759A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63143 AN: 151854 Hom.: 15446 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.0224

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.416 AC: 63212 AN: 151972 Hom.: 15469 Cov.: 31 AF XY: 0.402 AC XY: 29895 AN XY: 74292

African (AFR) AF: 0.658 AC: 27264 AN: 41420

American (AMR) AF: 0.350 AC: 5337 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1551 AN: 3472

East Asian (EAS) AF: 0.0223 AC: 115 AN: 5166

South Asian (SAS) AF: 0.236 AC: 1140 AN: 4826

European-Finnish (FIN) AF: 0.194 AC: 2051 AN: 10564

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24228 AN: 67966

Other (OTH) AF: 0.443 AC: 932 AN: 2106

Alfa AF: 0.392 Hom.: 35186

Bravo AF: 0.442

Asia WGS AF: 0.203 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.37
DANN	Benign	0.81
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1479211; hg19: chr5-117566290;