rs7960664

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02458	ENST00000549278.2	n.296-26191C>T		intron_variant, non_coding_transcript_variant		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;