chr2-58974894-G-C

Variant names:

• chr2-58974894-G-C
• rs111835151
• ENST00000422723.6:n.884-39436G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000422723.6(LINC01122):​n.884-39436G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0257 in 149,100 control chromosomes in the GnomAD database, including 69 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 0.026 (69 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• 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=-0.72).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0257 (3826/149100) while in subpopulation NFE AF = 0.0371 (2506/67534). AF 95% confidence interval is 0.0359. There are 69 homozygotes in GnomAd4. There are 1768 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 69 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422723.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	NR_033873.1		n.834-29055G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	ENST00000422723.6	TSL:3	n.884-39436G>C		intron	N/A
	LINC01122	ENST00000427421.5	TSL:2	n.834-29055G>C		intron	N/A
	LINC01122	ENST00000449448.6	TSL:3	n.639-29055G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0257 AC: 3829 AN: 149006 Hom.: 70 Cov.: 32

Gnomad AFR AF: 0.00738

Gnomad AMI AF: 0.0210

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00781

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0260

Gnomad NFE AF: 0.0371

Gnomad OTH AF: 0.0277

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

GnomAD4 genome AF: 0.0257 AC: 3826 AN: 149100 Hom.: 69 Cov.: 32 AF XY: 0.0244 AC XY: 1768 AN XY: 72446

African (AFR) AF: 0.00736 AC: 298 AN: 40498

American (AMR) AF: 0.0259 AC: 386 AN: 14888

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5086

South Asian (SAS) AF: 0.00784 AC: 37 AN: 4722

European-Finnish (FIN) AF: 0.0200 AC: 193 AN: 9634

Middle Eastern (MID) AF: 0.0245 AC: 7 AN: 286

European-Non Finnish (NFE) AF: 0.0371 AC: 2506 AN: 67534

Other (OTH) AF: 0.0269 AC: 56 AN: 2078

Alfa AF: 0.0274 Hom.: 8

Bravo AF: 0.0262

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	14
DANN	Benign	0.69
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs111835151; hg19: chr2-59202029;