3-165762312-G-A

Variant names:

• chr3-165762312-G-A
• rs6445035
• ENST00000651449.1:n.1008-83580G>A

Variant summary

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

The ENST00000651449.1(LINC01322):​n.1008-83580G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,902 control chromosomes in the GnomAD database, including 2,583 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 0.19 (2583 hom., cov: 32)
• Consequence: LINC01322 ENST00000651449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 15 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651449.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01322	ENST00000651449.1		n.1008-83580G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28112 AN: 151786 Hom.: 2582 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.185 AC: 28113 AN: 151902 Hom.: 2583 Cov.: 32 AF XY: 0.183 AC XY: 13602 AN XY: 74254

African (AFR) AF: 0.194 AC: 8050 AN: 41436

American (AMR) AF: 0.140 AC: 2127 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 612 AN: 3462

East Asian (EAS) AF: 0.117 AC: 603 AN: 5162

South Asian (SAS) AF: 0.168 AC: 808 AN: 4814

European-Finnish (FIN) AF: 0.168 AC: 1772 AN: 10564

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13502 AN: 67910

Other (OTH) AF: 0.183 AC: 386 AN: 2108

Alfa AF: 0.193 Hom.: 4686

Bravo AF: 0.187

Asia WGS AF: 0.142 AC: 497 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.75
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs6445035; hg19: chr3-165480100;