chr3-152112520-A-G

Variant names:

• chr3-152112520-A-G
• rs11712066
• ENST00000781909.1:n.23-38806T>C

Variant summary

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

The ENST00000781909.1(LINC02917):​n.23-38806T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,118 control chromosomes in the GnomAD database, including 2,304 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 0.15 (2304 hom., cov: 32)
• Consequence: LINC02917 ENST00000781909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 20 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000781909.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02917	ENST00000781909.1		n.23-38806T>C		intron	N/A
	LINC02917	ENST00000781910.1		n.270+748T>C		intron	N/A
	LINC02917	ENST00000781911.1		n.237+748T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22758 AN: 152000 Hom.: 2306 Cov.: 32

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.150 AC: 22756 AN: 152118 Hom.: 2304 Cov.: 32 AF XY: 0.146 AC XY: 10819 AN XY: 74346

African (AFR) AF: 0.0405 AC: 1684 AN: 41540

American (AMR) AF: 0.124 AC: 1887 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3462

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5190

South Asian (SAS) AF: 0.0951 AC: 459 AN: 4824

European-Finnish (FIN) AF: 0.221 AC: 2339 AN: 10570

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15257 AN: 67942

Other (OTH) AF: 0.158 AC: 335 AN: 2116

Alfa AF: 0.196 Hom.: 10688

Bravo AF: 0.139

Asia WGS AF: 0.0500 AC: 174 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs11712066; hg19: chr3-151830309;