rs379212

Variant names:

• chr5-61646103-A-G
• rs379212
• ENST00000505642.6:n.148+2703A>G

Variant summary

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

The ENST00000505642.6(LINC03122):​n.148+2703A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,202 control chromosomes in the GnomAD database, including 1,812 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 (1812 hom., cov: 32)
• Consequence: LINC03122 ENST00000505642.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.64
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505642.6. 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_126523.1		n.140+2703A>G		intron	N/A
	LINC03122	NR_126524.1		n.140+2703A>G		intron	N/A
	LINC03122	NR_126525.1		n.66+8257A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03122	ENST00000505642.6	TSL:2	n.148+2703A>G		intron	N/A
	LINC03122	ENST00000507461.2	TSL:4	n.139+8257A>G		intron	N/A
	LINC03122	ENST00000510414.4	TSL:3	n.161+2703A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22579 AN: 152084 Hom.: 1809 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.148 AC: 22602 AN: 152202 Hom.: 1812 Cov.: 32 AF XY: 0.146 AC XY: 10897 AN XY: 74402

African (AFR) AF: 0.115 AC: 4762 AN: 41536

American (AMR) AF: 0.130 AC: 1989 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3470

East Asian (EAS) AF: 0.124 AC: 638 AN: 5146

South Asian (SAS) AF: 0.0741 AC: 357 AN: 4820

European-Finnish (FIN) AF: 0.162 AC: 1720 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12235 AN: 68004

Other (OTH) AF: 0.147 AC: 310 AN: 2114

Alfa AF: 0.168 Hom.: 9511

Bravo AF: 0.145

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.69
PhyloP100		2.6
Mutation Taster		=100/0	polymorphism (auto)

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: rs379212;

hg19: chr5-60941930;