rs7592415

Positions:

• chr2-58845381-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_033873.1(LINC01122):​n.248-5049A>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 0.324 in 151,918 control chromosomes in the GnomAD database, including 9,239 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 0.32 (9239 hom., cov: 32)
• Consequence: LINC01122 NR_033873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01122	NR_033873.1	n.248-5049A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01122	ENST00000452840.5	n.258-5049A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49097 AN: 151800 Hom.: 9214 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.324 AC: 49169 AN: 151918 Hom.: 9239 Cov.: 32 AF XY: 0.323 AC XY: 24010 AN XY: 74238

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.312

Alfa AF: 0.250 Hom.: 10224

Bravo AF: 0.328

Asia WGS AF: 0.314 AC: 1092 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	6.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7592415; hg19: chr2-59072516;