rs10079352

Variant names:

• chr5-118158945-G-A
• rs10079352
• ENST00000509367.3:n.303-28520G>A

Variant summary

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

The ENST00000509367.3(LINC02147):​n.303-28520G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,880 control chromosomes in the GnomAD database, including 30,369 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 0.60 (30369 hom., cov: 31)
• Consequence: LINC02147 ENST00000509367.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 14 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=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 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.171-106409G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02147	ENST00000509367.3	TSL:2	n.303-28520G>A		intron	N/A
	LINC02147	ENST00000509669.1	TSL:3	n.255-28520G>A		intron	N/A
	LINC02147	ENST00000657852.1		n.268-47775G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90343 AN: 151762 Hom.: 30313 Cov.: 31

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.596 AC: 90449 AN: 151880 Hom.: 30369 Cov.: 31 AF XY: 0.582 AC XY: 43143 AN XY: 74188

African (AFR) AF: 0.889 AC: 36877 AN: 41482

American (AMR) AF: 0.450 AC: 6850 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1875 AN: 3468

East Asian (EAS) AF: 0.0216 AC: 111 AN: 5134

South Asian (SAS) AF: 0.400 AC: 1925 AN: 4808

European-Finnish (FIN) AF: 0.416 AC: 4386 AN: 10552

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36414 AN: 67906

Other (OTH) AF: 0.596 AC: 1258 AN: 2110

Alfa AF: 0.546 Hom.: 98738

Bravo AF: 0.611

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.2
DANN	Benign	0.62
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10079352; hg19: chr5-117494640;