3-165562421-C-T

Variant names:

• chr3-165562421-C-T
• rs1523288
• ENST00000470138.5:n.408-18438C>T

Variant summary

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

The ENST00000470138.5(LINC01322):​n.408-18438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 150,570 control chromosomes in the GnomAD database, including 34,087 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 0.67 (34087 hom., cov: 29)
• Consequence: LINC01322 ENST00000470138.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 11 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000470138.5. 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
	LINC01322	ENST00000470138.5	TSL:4	n.408-18438C>T		intron	N/A
	LINC01322	ENST00000496693.1	TSL:5	n.312+13272C>T		intron	N/A
	LINC01322	ENST00000651449.1		n.374+2047C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100098 AN: 150446 Hom.: 34049 Cov.: 29

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.665 AC: 100181 AN: 150570 Hom.: 34087 Cov.: 29 AF XY: 0.662 AC XY: 48655 AN XY: 73476

African (AFR) AF: 0.796 AC: 32388 AN: 40668

American (AMR) AF: 0.635 AC: 9633 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2202 AN: 3466

East Asian (EAS) AF: 0.459 AC: 2326 AN: 5072

South Asian (SAS) AF: 0.527 AC: 2517 AN: 4778

European-Finnish (FIN) AF: 0.579 AC: 6002 AN: 10360

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.632 AC: 42852 AN: 67770

Other (OTH) AF: 0.672 AC: 1406 AN: 2092

Alfa AF: 0.641 Hom.: 52390

Bravo AF: 0.676

Asia WGS AF: 0.496 AC: 1717 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.24
DANN	Benign	0.32
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1523288; hg19: chr3-165280209;