rs12468708

Variant names:

• chr2-58659904-C-A
• rs12468708
• ENST00000422723.6:n.325+3193C>A

Variant summary

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

The ENST00000422723.6(LINC01122):​n.325+3193C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,024 control chromosomes in the GnomAD database, including 12,143 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 0.39 (12143 hom., cov: 33)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.247+3193C>A		intron_variant	Intron 2 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.325+3193C>A		intron_variant	Intron 3 of 10	3
LINC01122	ENST00000422793.4	n.196+3193C>A		intron_variant	Intron 3 of 6	5
LINC01122	ENST00000427421.5	n.247+3193C>A		intron_variant	Intron 2 of 13	2

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58829 AN: 151906 Hom.: 12140 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.387 AC: 58858 AN: 152024 Hom.: 12143 Cov.: 33 AF XY: 0.396 AC XY: 29414 AN XY: 74320

African (AFR) AF: 0.244 AC: 10137 AN: 41472

American (AMR) AF: 0.460 AC: 7019 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1352 AN: 3470

East Asian (EAS) AF: 0.575 AC: 2967 AN: 5156

South Asian (SAS) AF: 0.417 AC: 2011 AN: 4818

European-Finnish (FIN) AF: 0.521 AC: 5507 AN: 10568

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28709 AN: 67964

Other (OTH) AF: 0.377 AC: 795 AN: 2108

Alfa AF: 0.412 Hom.: 7523

Bravo AF: 0.378

Asia WGS AF: 0.435 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.4
DANN	Benign	0.66
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs12468708; hg19: chr2-58887039;