rs601007

Variant names:

• chr3-152148672-T-C
• rs601007
• ENST00000482382.2:n.771+2994A>G

Variant summary

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

The ENST00000482382.2(LINC02917):​n.771+2994A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,110 control chromosomes in the GnomAD database, including 7,539 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 0.30 (7539 hom., cov: 33)
• Consequence: LINC02917 ENST00000482382.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 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.344+2994A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02917	ENST00000482382.2	TSL:4	n.771+2994A>G		intron	N/A
	LINC02917	ENST00000781727.1		n.330+26127A>G		intron	N/A
	LINC02917	ENST00000781728.1		n.92-30005A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46107 AN: 151990 Hom.: 7537 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.303 AC: 46150 AN: 152110 Hom.: 7539 Cov.: 33 AF XY: 0.301 AC XY: 22381 AN XY: 74376

African (AFR) AF: 0.183 AC: 7613 AN: 41502

American (AMR) AF: 0.319 AC: 4872 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 972 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1506 AN: 5182

South Asian (SAS) AF: 0.238 AC: 1149 AN: 4822

European-Finnish (FIN) AF: 0.369 AC: 3901 AN: 10574

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

European-Non Finnish (NFE) AF: 0.368 AC: 25001 AN: 67970

Other (OTH) AF: 0.321 AC: 679 AN: 2112

Alfa AF: 0.330 Hom.: 1162

Bravo AF: 0.297

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.52
PhyloP100		-0.91

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: rs601007;

hg19: chr3-151866461;