rs7960664

Variant names:

• chr12-89077458-G-A
• rs7960664
• ENST00000549278.2:n.296-26191C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-89077458-G-A
• chr12-89077458-G-T

Variant summary

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

The ENST00000549278.2(LINC02458):​n.296-26191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,198 control chromosomes in the GnomAD database, including 53,721 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 0.84 (53721 hom., cov: 33)
• Consequence: LINC02458 ENST00000549278.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 2 publications found

Genes affected

LINC02458 (HGNC:53394): (long intergenic non-protein coding RNA 2458)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549278.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02458	ENST00000549278.2	TSL:4	n.296-26191C>T		intron	N/A
	LINC02458	ENST00000846494.1		n.355+18072C>T		intron	N/A
	LINC02458	ENST00000846495.1		n.408+18072C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127479 AN: 152080 Hom.: 53677 Cov.: 33

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.838 AC: 127582 AN: 152198 Hom.: 53721 Cov.: 33 AF XY: 0.842 AC XY: 62665 AN XY: 74416

African (AFR) AF: 0.791 AC: 32850 AN: 41512

American (AMR) AF: 0.863 AC: 13207 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2903 AN: 3472

East Asian (EAS) AF: 0.666 AC: 3428 AN: 5150

South Asian (SAS) AF: 0.853 AC: 4115 AN: 4824

European-Finnish (FIN) AF: 0.922 AC: 9783 AN: 10610

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58567 AN: 68014

Other (OTH) AF: 0.828 AC: 1750 AN: 2114

Alfa AF: 0.851 Hom.: 152296

Bravo AF: 0.831

Asia WGS AF: 0.747 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.54
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs7960664; hg19: chr12-89471235;