rs17031166

chr2-65939930-G-C

Variant summary

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

The ENST00000606978.5(LINC02934):n.787-31618G>C variant causes a intron, non coding transcript 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 ENST00000606978.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02934	XR_007086567.1	n.128+17861G>C		intron_variant, non_coding_transcript_variant
LINC02934	XR_007086575.1	n.128+17861G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02934	ENST00000606978.5	n.787-31618G>C		intron_variant, non_coding_transcript_variant		5
LINC02934	ENST00000606556.1	n.141+17861G>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.330

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	12
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17031166; hg19: chr2-66167064;