rs9318189

Variant names:

• chr13-73550101-C-T
• rs9318189
• ENST00000443621.2:n.136-3260G>A

Variant summary

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

The ENST00000443621.2(LINC00393):​n.136-3260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 151,950 control chromosomes in the GnomAD database, including 1,597 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 0.089 (1597 hom., cov: 32)
• Consequence: LINC00393 ENST00000443621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 0 publications found

Genes affected

LINC00393 (HGNC:42721): (long intergenic non-protein coding RNA 393)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443621.2. 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
	LINC00393	NR_184171.1		n.143-3260G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00393	ENST00000443621.2	TSL:3	n.136-3260G>A		intron	N/A
	LINC00393	ENST00000452852.2	TSL:3	n.32-3260G>A		intron	N/A
	LINC00393	ENST00000647940.1		n.129-3260G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0893 AC: 13554 AN: 151834 Hom.: 1597 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0894 AC: 13577 AN: 151950 Hom.: 1597 Cov.: 32 AF XY: 0.0964 AC XY: 7160 AN XY: 74256

African (AFR) AF: 0.154 AC: 6372 AN: 41412

American (AMR) AF: 0.0427 AC: 652 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3470

East Asian (EAS) AF: 0.599 AC: 3090 AN: 5156

South Asian (SAS) AF: 0.165 AC: 792 AN: 4812

European-Finnish (FIN) AF: 0.0891 AC: 936 AN: 10504

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0185 AC: 1257 AN: 68004

Other (OTH) AF: 0.0719 AC: 152 AN: 2114

Alfa AF: 0.0567 Hom.: 82

Bravo AF: 0.0916

Asia WGS AF: 0.316 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.44
PhyloP100		-2.0

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: rs9318189;

hg19: chr13-74124238;

COSMIC: COSV107531043;