rs6719683

chr2-58867055-G-Achr2-58867055-G-T

Variant summary

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

The NR_033873.1(LINC01122):n.424+16449G>A 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 0.337 in 151,828 control chromosomes in the GnomAD database, including 9,478 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 0.34 (9478 hom., cov: 32)
• Consequence: LINC01122 NR_033873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

LINC01122 (HGNC:49267): (long intergenic non-protein coding RNA 1122)

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 = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01122	NR_033873.1	n.424+16449G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01122	ENST00000452840.5	n.434+16449G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51142 AN: 151710 Hom.: 9462 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.411

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: 0.337 AC: 51209 AN: 151828 Hom.: 9478 Cov.: 32 AF XY: 0.337 AC XY: 25026 AN XY: 74194

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.327

Alfa AF: 0.273 Hom.: 12038

Bravo AF: 0.346

Asia WGS AF: 0.373 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6719683; hg19: chr2-59094190;