rs10169462

Variant names:

• chr2-59225027-C-T
• rs10169462
• ENST00000409590.1:n.67+7253C>T

Variant summary

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

The ENST00000409590.1(LINC01122):​n.67+7253C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,084 control chromosomes in the GnomAD database, including 1,682 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 0.15 (1682 hom., cov: 32)
• Consequence: LINC01122 ENST00000409590.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 1 publications found

Genes affected

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

ENSG00000233891 (HGNC:):

LINC01793 (HGNC:52583): (long intergenic non-protein coding RNA 1793)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409590.1. 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
	LINC01793	NR_110219.1		n.67+7253C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	ENST00000409590.1	TSL:2	n.67+7253C>T		intron	N/A
	LINC01122	ENST00000422723.6	TSL:3	n.1151-88706C>T		intron	N/A
	ENSG00000233891	ENST00000606382.1	TSL:5	n.434-6303G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22213 AN: 151966 Hom.: 1683 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.146 AC: 22230 AN: 152084 Hom.: 1682 Cov.: 32 AF XY: 0.147 AC XY: 10954 AN XY: 74340

African (AFR) AF: 0.121 AC: 5044 AN: 41516

American (AMR) AF: 0.104 AC: 1582 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3470

East Asian (EAS) AF: 0.123 AC: 635 AN: 5160

South Asian (SAS) AF: 0.148 AC: 715 AN: 4818

European-Finnish (FIN) AF: 0.218 AC: 2300 AN: 10574

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11030 AN: 67970

Other (OTH) AF: 0.134 AC: 282 AN: 2110

Alfa AF: 0.157 Hom.: 675

Bravo AF: 0.135

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.073
DANN	Benign	0.34
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10169462; hg19: chr2-59452162;