rs1466011

Variant names:

• chr5-61726825-C-T
• rs1466011
• ENST00000507461.2:n.140-21777C>T

Variant summary

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

The ENST00000510414.4(LINC03122):​n.405-3221C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,008 control chromosomes in the GnomAD database, including 2,533 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 0.17 (2533 hom., cov: 32)
• Consequence: LINC03122 ENST00000510414.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

Genes affected

LINC03122 (HGNC:26744): (long intergenic non-protein coding RNA 3122) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510414.4. 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
	LINC03122	NR_126524.1		n.384-3221C>T		intron	N/A
	LINC03122	NR_126525.1		n.67-3221C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03122	ENST00000507461.2	TSL:4	n.140-21777C>T		intron	N/A
	LINC03122	ENST00000510414.4	TSL:3	n.405-3221C>T		intron	N/A
	LINC03122	ENST00000511407.1	TSL:4	n.67-3221C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25825 AN: 151890 Hom.: 2534 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.170 AC: 25825 AN: 152008 Hom.: 2533 Cov.: 32 AF XY: 0.167 AC XY: 12412 AN XY: 74312

African (AFR) AF: 0.0825 AC: 3421 AN: 41450

American (AMR) AF: 0.142 AC: 2176 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3466

East Asian (EAS) AF: 0.146 AC: 752 AN: 5154

South Asian (SAS) AF: 0.127 AC: 611 AN: 4810

European-Finnish (FIN) AF: 0.208 AC: 2202 AN: 10568

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 14996 AN: 67976

Other (OTH) AF: 0.184 AC: 388 AN: 2104

Alfa AF: 0.200 Hom.: 1530

Bravo AF: 0.163

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.88
DANN	Benign	0.58
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1466011; hg19: chr5-61022652;