2-58606358-A-G

Variant names:

• chr2-58606358-A-G
• rs6731302
• ENST00000422723.6:n.264-50292A>G

Variant summary

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

The ENST00000422723.6(LINC01122):​n.264-50292A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,914 control chromosomes in the GnomAD database, including 30,172 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 0.62 (30172 hom., cov: 31)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 18 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=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.186-50292A>G		intron_variant	Intron 1 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.264-50292A>G		intron_variant	Intron 2 of 10	3
LINC01122	ENST00000422793.4	n.135-50292A>G		intron_variant	Intron 2 of 6	5
LINC01122	ENST00000427421.5	n.186-50292A>G		intron_variant	Intron 1 of 13	2

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94746 AN: 151796 Hom.: 30115 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.624 AC: 94857 AN: 151914 Hom.: 30172 Cov.: 31 AF XY: 0.622 AC XY: 46171 AN XY: 74230

African (AFR) AF: 0.747 AC: 30954 AN: 41428

American (AMR) AF: 0.522 AC: 7958 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2091 AN: 3468

East Asian (EAS) AF: 0.782 AC: 4031 AN: 5156

South Asian (SAS) AF: 0.605 AC: 2914 AN: 4816

European-Finnish (FIN) AF: 0.573 AC: 6042 AN: 10542

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.574 AC: 39011 AN: 67944

Other (OTH) AF: 0.597 AC: 1259 AN: 2108

Alfa AF: 0.602 Hom.: 41206

Bravo AF: 0.625

Asia WGS AF: 0.632 AC: 2196 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	17
DANN	Benign	0.82
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6731302; hg19: chr2-58833493;