rs1024766

Positions:

• chr2-58997330-G-A

Variant summary

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

The ENST00000427421.5(LINC01122):​n.834-6619G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,924 control chromosomes in the GnomAD database, including 21,928 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 0.52 (21928 hom., cov: 32)
• Consequence: LINC01122 ENST00000427421.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

Genes affected

LINC01122 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.834-6619G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000427421.5	n.834-6619G>A		intron_variant		2
LINC01122	ENST00000449448.6	n.639-6619G>A		intron_variant		3
LINC01122	ENST00000452840.5	n.816-6619G>A		intron_variant		5
LINC01122	ENST00000650056.1	n.674-6619G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78516 AN: 151806 Hom.: 21887 Cov.: 32

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.517 AC: 78609 AN: 151924 Hom.: 21928 Cov.: 32 AF XY: 0.511 AC XY: 37918 AN XY: 74262

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.477

Alfa AF: 0.477 Hom.: 10329

Bravo AF: 0.523

Asia WGS AF: 0.451 AC: 1571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024766; hg19: chr2-59224465;