chr9-90397568-T-C

Variant names:

• chr9-90397568-T-C
• rs7858079
• ENST00000425666.3:n.255-13847A>G

Variant summary

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

The ENST00000425666.3(LINC01508):​n.255-13847A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,112 control chromosomes in the GnomAD database, including 30,548 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 0.62 (30548 hom., cov: 32)
• Consequence: LINC01508 ENST00000425666.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807
• Publications: 0 publications found

Genes affected

LINC01508 (HGNC:51190): (long intergenic non-protein coding RNA 1508)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425666.3. 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
	LINC01508	NR_109795.1		n.60-13847A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01508	ENST00000425666.3	TSL:3	n.255-13847A>G		intron	N/A
	LINC01508	ENST00000436671.2	TSL:3	n.76-11985A>G		intron	N/A
	LINC01508	ENST00000659218.1		n.200-13847A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94949 AN: 151994 Hom.: 30536 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.624 AC: 94991 AN: 152112 Hom.: 30548 Cov.: 32 AF XY: 0.629 AC XY: 46812 AN XY: 74378

African (AFR) AF: 0.467 AC: 19376 AN: 41456

American (AMR) AF: 0.729 AC: 11151 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2355 AN: 3470

East Asian (EAS) AF: 0.750 AC: 3882 AN: 5178

South Asian (SAS) AF: 0.651 AC: 3141 AN: 4822

European-Finnish (FIN) AF: 0.705 AC: 7448 AN: 10572

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45396 AN: 67996

Other (OTH) AF: 0.627 AC: 1321 AN: 2108

Alfa AF: 0.637 Hom.: 5108

Bravo AF: 0.619

Asia WGS AF: 0.696 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.61
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs7858079; hg19: chr9-93159850;