rs13242060

Variant names:

• chr7-17519264-T-C
• rs13242060
• ENST00000451792.1:n.159-35730A>G

Variant summary

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

The ENST00000451792.1(LINC02889):​n.159-35730A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,204 control chromosomes in the GnomAD database, including 1,038 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 0.10 (1038 hom., cov: 32)
• Consequence: LINC02889 ENST00000451792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 0 publications found

Genes affected

LINC02889 (HGNC:55071): (long intergenic non-protein coding RNA 2889)

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 (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451792.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02889	NR_110013.1		n.159-35730A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02889	ENST00000451792.1	TSL:3	n.159-35730A>G		intron	N/A
	LINC02889	ENST00000454003.2	TSL:3	n.52+4833A>G		intron	N/A
	LINC02889	ENST00000636929.1	TSL:5	n.79+4833A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15320 AN: 152086 Hom.: 1040 Cov.: 32

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.101 AC: 15316 AN: 152204 Hom.: 1038 Cov.: 32 AF XY: 0.106 AC XY: 7854 AN XY: 74424

African (AFR) AF: 0.0229 AC: 950 AN: 41556

American (AMR) AF: 0.171 AC: 2610 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 449 AN: 3462

East Asian (EAS) AF: 0.119 AC: 614 AN: 5176

South Asian (SAS) AF: 0.212 AC: 1020 AN: 4816

European-Finnish (FIN) AF: 0.141 AC: 1499 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7815 AN: 67994

Other (OTH) AF: 0.108 AC: 229 AN: 2112

Alfa AF: 0.110 Hom.: 220

Bravo AF: 0.0979

Asia WGS AF: 0.150 AC: 520 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	8.2
DANN	Benign	0.57
PhyloP100		-0.54

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13242060;

hg19: chr7-17558888;