9-103221395-G-A

Variant names:

• chr9-103221395-G-A
• rs1448576
• ENST00000411575.5:n.870+6319C>T

Variant summary

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

The ENST00000411575.5(LINC01492):​n.870+6319C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,794 control chromosomes in the GnomAD database, including 14,263 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 0.43 (14263 hom., cov: 31)
• Consequence: LINC01492 ENST00000411575.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 2 publications found

Genes affected

LINC01492 (HGNC:51149): (long intergenic non-protein coding RNA 1492)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411575.5. 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
	LINC01492	NR_121578.1		n.869+6319C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01492	ENST00000411575.5	TSL:1	n.870+6319C>T		intron	N/A
	LINC01492	ENST00000425157.3	TSL:5	n.388+6319C>T		intron	N/A
	LINC01492	ENST00000806271.1		n.513+6319C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65166 AN: 151676 Hom.: 14258 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.429 AC: 65183 AN: 151794 Hom.: 14263 Cov.: 31 AF XY: 0.432 AC XY: 32042 AN XY: 74154

African (AFR) AF: 0.343 AC: 14206 AN: 41418

American (AMR) AF: 0.494 AC: 7512 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1434 AN: 3462

East Asian (EAS) AF: 0.413 AC: 2131 AN: 5156

South Asian (SAS) AF: 0.340 AC: 1640 AN: 4820

European-Finnish (FIN) AF: 0.524 AC: 5526 AN: 10538

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.459 AC: 31156 AN: 67888

Other (OTH) AF: 0.419 AC: 883 AN: 2108

Alfa AF: 0.365 Hom.: 1574

Bravo AF: 0.425

Asia WGS AF: 0.376 AC: 1304 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.56
PhyloP100		-0.66

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: rs1448576;

hg19: chr9-105983677;