rs325738

Variant names:

• chr3-152128519-G-A
• rs325738
• ENST00000482382.2:n.772-9852C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-152128519-G-A
• chr3-152128519-G-C
• chr3-152128519-G-T

Variant summary

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

The ENST00000482382.2(LINC02917):​n.772-9852C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,034 control chromosomes in the GnomAD database, including 7,708 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 0.31 (7708 hom., cov: 32)
• Consequence: LINC02917 ENST00000482382.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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: ENST00000482382.2. 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
	LINC02917	NR_186000.1		n.345-9852C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02917	ENST00000482382.2	TSL:4	n.772-9852C>T		intron	N/A
	LINC02917	ENST00000781727.1		n.331-9852C>T		intron	N/A
	LINC02917	ENST00000781728.1		n.92-9852C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46777 AN: 151916 Hom.: 7707 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.308 AC: 46818 AN: 152034 Hom.: 7708 Cov.: 32 AF XY: 0.306 AC XY: 22734 AN XY: 74326

African (AFR) AF: 0.192 AC: 7962 AN: 41454

American (AMR) AF: 0.319 AC: 4864 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3472

East Asian (EAS) AF: 0.311 AC: 1611 AN: 5172

South Asian (SAS) AF: 0.242 AC: 1164 AN: 4818

European-Finnish (FIN) AF: 0.380 AC: 4013 AN: 10568

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

European-Non Finnish (NFE) AF: 0.369 AC: 25090 AN: 67972

Other (OTH) AF: 0.324 AC: 684 AN: 2110

Alfa AF: 0.339 Hom.: 20794

Bravo AF: 0.300

Asia WGS AF: 0.266 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.97
DANN	Benign	0.44
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs325738;

hg19: chr3-151846308;