rs17031166

Variant names:

• chr2-65939930-G-C
• rs17031166
• ENST00000606556.1:n.141+17861G>C

Variant summary

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

The ENST00000606556.1(LINC02934):​n.141+17861G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,050 control chromosomes in the GnomAD database, including 8,308 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 0.33 (8308 hom., cov: 32)
• Consequence: LINC02934 ENST00000606556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 2 publications found

Genes affected

LINC02934 (HGNC:55913): (long intergenic non-protein coding RNA 2934)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606556.1. 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
	LINC02934	NR_187140.1		n.192+17861G>C		intron	N/A
	LINC02934	NR_187141.1		n.61-31618G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02934	ENST00000606556.1	TSL:2	n.141+17861G>C		intron	N/A
	LINC02934	ENST00000606978.5	TSL:5	n.787-31618G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49446 AN: 151932 Hom.: 8291 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.326 AC: 49502 AN: 152050 Hom.: 8308 Cov.: 32 AF XY: 0.328 AC XY: 24407 AN XY: 74320

African (AFR) AF: 0.270 AC: 11179 AN: 41478

American (AMR) AF: 0.424 AC: 6484 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3472

East Asian (EAS) AF: 0.527 AC: 2717 AN: 5154

South Asian (SAS) AF: 0.334 AC: 1612 AN: 4824

European-Finnish (FIN) AF: 0.319 AC: 3371 AN: 10558

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22219 AN: 67966

Other (OTH) AF: 0.330 AC: 696 AN: 2112

Alfa AF: 0.322 Hom.: 1004

Bravo AF: 0.333

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	12
DANN	Benign	0.58
PhyloP100		0.069

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: rs17031166;

hg19: chr2-66167064;