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. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02458	ENST00000549278.2	n.296-26191C>T		intron_variant	Intron 2 of 6	4

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

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.828

Alfa AF: 0.854 Hom.: 91324

Bravo AF: 0.831

Asia WGS AF: 0.747 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7960664; hg19: chr12-89471235;