rs9309394

Variant names:

• chr2-66781497-T-C
• rs9309394
• ENST00000715601.1:n.185-66489T>C

Variant summary

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

The ENST00000715601.1(LINC01798):​n.185-66489T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,002 control chromosomes in the GnomAD database, including 27,042 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 0.58 (27042 hom., cov: 32)
• Consequence: LINC01798 ENST00000715601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 3 publications found

Genes affected

LINC01798 (HGNC:52588): (long intergenic non-protein coding RNA 1798)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715601.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01798	ENST00000715601.1		n.185-66489T>C		intron	N/A
	LINC01798	ENST00000758432.1		n.185-66489T>C		intron	N/A
	LINC01798	ENST00000758436.1		n.247-66489T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88555 AN: 151884 Hom.: 27017 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.583 AC: 88630 AN: 152002 Hom.: 27042 Cov.: 32 AF XY: 0.572 AC XY: 42505 AN XY: 74272

African (AFR) AF: 0.773 AC: 32075 AN: 41472

American (AMR) AF: 0.516 AC: 7880 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3464

East Asian (EAS) AF: 0.428 AC: 2206 AN: 5150

South Asian (SAS) AF: 0.598 AC: 2879 AN: 4812

European-Finnish (FIN) AF: 0.407 AC: 4297 AN: 10570

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35812 AN: 67950

Other (OTH) AF: 0.577 AC: 1217 AN: 2110

Alfa AF: 0.550 Hom.: 14657

Bravo AF: 0.596

Asia WGS AF: 0.539 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.39
PhyloP100		-1.0

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: rs9309394;

hg19: chr2-67008629;