3-152175239-A-G

Variant names:

• chr3-152175239-A-G
• rs325762
• ENST00000689682.2:n.174-366T>C

Variant summary

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

The ENST00000689682.2(LINC02917):​n.174-366T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,784 control chromosomes in the GnomAD database, including 8,119 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 0.32 (8119 hom., cov: 32)
• Consequence: LINC02917 ENST00000689682.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 3 publications found

Genes affected

LINC02917 (HGNC:55643): (long intergenic non-protein coding RNA 2917)

LOC101928166 (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 (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000689682.2. 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
	LOC101928166	NR_136178.1		n.58-366T>C		intron	N/A
	LINC02917	NR_186000.1		n.56-23285T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02917	ENST00000689682.2		n.174-366T>C		intron	N/A
	LINC02917	ENST00000781727.1		n.256-366T>C		intron	N/A
	LINC02917	ENST00000781728.1		n.91+30134T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48801 AN: 151666 Hom.: 8117 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.322 AC: 48850 AN: 151784 Hom.: 8119 Cov.: 32 AF XY: 0.318 AC XY: 23620 AN XY: 74184

African (AFR) AF: 0.248 AC: 10260 AN: 41418

American (AMR) AF: 0.322 AC: 4887 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 986 AN: 3460

East Asian (EAS) AF: 0.288 AC: 1482 AN: 5150

South Asian (SAS) AF: 0.239 AC: 1153 AN: 4820

European-Finnish (FIN) AF: 0.369 AC: 3899 AN: 10576

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25028 AN: 67860

Other (OTH) AF: 0.333 AC: 700 AN: 2102

Alfa AF: 0.347 Hom.: 3651

Bravo AF: 0.317

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.63
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs325762; hg19: chr3-151893028;