rs6449558

Variant names:

• chr5-61789725-C-T
• rs6449558
• ENST00000667197.1:n.814-1049C>T

Variant summary

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

The ENST00000667197.1(LINC03122):​n.814-1049C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,950 control chromosomes in the GnomAD database, including 11,961 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 0.38 (11961 hom., cov: 31)
• Consequence: LINC03122 ENST00000667197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03122	ENST00000667197.1	n.814-1049C>T		intron_variant	Intron 6 of 6
LINC03122	ENST00000797193.1	n.571-8977C>T		intron_variant	Intron 5 of 10

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57209 AN: 151830 Hom.: 11945 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.377 AC: 57260 AN: 151950 Hom.: 11961 Cov.: 31 AF XY: 0.371 AC XY: 27576 AN XY: 74288

African (AFR) AF: 0.573 AC: 23738 AN: 41410

American (AMR) AF: 0.310 AC: 4742 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1380 AN: 5168

South Asian (SAS) AF: 0.377 AC: 1812 AN: 4808

European-Finnish (FIN) AF: 0.238 AC: 2514 AN: 10548

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20870 AN: 67944

Other (OTH) AF: 0.342 AC: 722 AN: 2110

Alfa AF: 0.328 Hom.: 36640

Bravo AF: 0.388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.71
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs6449558; hg19: chr5-61085552;