rs9298877

Variant names:

• chr9-26080403-T-A
• rs9298877
• ENST00000612217.2:n.153-11958T>A

Your query was ambiguous. Multiple possible variants found:

• chr9-26080403-T-A
• chr9-26080403-T-C
• chr9-26080403-T-G

Variant summary

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

The ENST00000612217.2(LINC03106):​n.153-11958T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,004 control chromosomes in the GnomAD database, including 16,947 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 0.46 (16947 hom., cov: 32)
• Consequence: LINC03106 ENST00000612217.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 2 publications found

Genes affected

LINC03106 (HGNC:56836): (long intergenic non-protein coding RNA 3106)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612217.2. 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
	LINC03106	NR_170894.1		n.153-11958T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03106	ENST00000612217.2	TSL:2	n.153-11958T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70134 AN: 151886 Hom.: 16947 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.461 AC: 70146 AN: 152004 Hom.: 16947 Cov.: 32 AF XY: 0.466 AC XY: 34641 AN XY: 74288

African (AFR) AF: 0.324 AC: 13449 AN: 41468

American (AMR) AF: 0.537 AC: 8202 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1506 AN: 3472

East Asian (EAS) AF: 0.671 AC: 3454 AN: 5146

South Asian (SAS) AF: 0.453 AC: 2184 AN: 4824

European-Finnish (FIN) AF: 0.568 AC: 5999 AN: 10560

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33722 AN: 67944

Other (OTH) AF: 0.479 AC: 1012 AN: 2112

Alfa AF: 0.462 Hom.: 2076

Bravo AF: 0.459

Asia WGS AF: 0.548 AC: 1897 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.27

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: rs9298877;

hg19: chr9-26080401;