rs286641

Positions:

• chr5-74072413-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183289.1(LINC02122):​n.510+11634A>G variant causes a intron, non coding transcript 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 NR_183289.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316

Genes affected

LINC02122 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02122	NR_183289.1	n.510+11634A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.324

Alfa AF: 0.274 Hom.: 11855

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs286641; hg19: chr5-73368238;