3-165524656-A-G

Variant names:

• chr3-165524656-A-G
• rs4387996
• ENST00000665369.1:n.2893A>G

Variant summary

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

The ENST00000665369.1(LINC01322):​n.2893A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 151,050 control chromosomes in the GnomAD database, including 39,277 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 0.72 (39277 hom., cov: 31)
• Consequence: LINC01322 ENST00000665369.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 4 publications found

Genes affected

LINC01322 (HGNC:50528): (long intergenic non-protein coding RNA 1322)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665369.1. 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
	LINC01322	NR_174098.1		n.824+13005A>G		intron	N/A
	LINC01322	NR_174099.1		n.451-14409A>G		intron	N/A
	LINC01322	NR_174100.1		n.1003+13005A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01322	ENST00000665369.1		n.2893A>G		non_coding_transcript_exon	Exon 6 of 6
	LINC01322	ENST00000470138.5	TSL:4	n.408-56203A>G		intron	N/A
	LINC01322	ENST00000651449.1		n.95-28731A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108028 AN: 150922 Hom.: 39239 Cov.: 31

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.727

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.716 AC: 108119 AN: 151050 Hom.: 39277 Cov.: 31 AF XY: 0.710 AC XY: 52363 AN XY: 73768

African (AFR) AF: 0.806 AC: 33383 AN: 41416

American (AMR) AF: 0.673 AC: 10175 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2563 AN: 3468

East Asian (EAS) AF: 0.476 AC: 2420 AN: 5080

South Asian (SAS) AF: 0.630 AC: 3001 AN: 4762

European-Finnish (FIN) AF: 0.638 AC: 6683 AN: 10472

Middle Eastern (MID) AF: 0.728 AC: 150 AN: 206

European-Non Finnish (NFE) AF: 0.704 AC: 47543 AN: 67522

Other (OTH) AF: 0.709 AC: 1477 AN: 2084

Alfa AF: 0.701 Hom.: 4454

Bravo AF: 0.720

Asia WGS AF: 0.548 AC: 1864 AN: 3396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.50
PhyloP100		0.083

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: rs4387996;

hg19: chr3-165242444;