rs601007

Positions:

• chr3-152148672-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000482382.1(LINC02917):​n.59+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 ENST00000482382.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

Genes affected

LINC02917 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02917	NR_186000.1	n.344+2994A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02917	ENST00000482382.1	n.59+2994A>G		intron_variant		4

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

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.321

Alfa AF: 0.337 Hom.: 1157

Bravo AF: 0.297

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs601007; hg19: chr3-151866461;