rs286641

Variant names:

• chr5-74072413-T-C
• rs286641
• ENST00000511395.2:n.598+11634A>G

Variant summary

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

The ENST00000511395.2(LINC02122):​n.598+11634A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,108 control chromosomes in the GnomAD database, including 7,793 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 0.31 (7793 hom., cov: 32)
• Consequence: LINC02122 ENST00000511395.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 3 publications found

Genes affected

LINC02122 (HGNC:52979): (long intergenic non-protein coding RNA 2122)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02122	NR_183289.1	n.510+11634A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02122	ENST00000511395.2	n.598+11634A>G		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46819 AN: 151990 Hom.: 7786 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.308 AC: 46843 AN: 152108 Hom.: 7793 Cov.: 32 AF XY: 0.303 AC XY: 22503 AN XY: 74358

African (AFR) AF: 0.435 AC: 18051 AN: 41476

American (AMR) AF: 0.304 AC: 4644 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3466

East Asian (EAS) AF: 0.160 AC: 829 AN: 5182

South Asian (SAS) AF: 0.141 AC: 682 AN: 4824

European-Finnish (FIN) AF: 0.259 AC: 2737 AN: 10580

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17659 AN: 67980

Other (OTH) AF: 0.324 AC: 685 AN: 2114

Alfa AF: 0.278 Hom.: 17298

Bravo AF: 0.323

Asia WGS AF: 0.162 AC: 567 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.99
DANN	Benign	0.78
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs286641; hg19: chr5-73368238;