4-123854317-C-T

Variant names:

• chr4-123854317-C-T
• rs3113392
• ENST00000515769.1:n.206-9258C>T

Variant summary

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

The ENST00000515769.1(LINC01091):​n.206-9258C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,556 control chromosomes in the GnomAD database, including 17,390 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 0.47 (17390 hom., cov: 31)
• Consequence: LINC01091 ENST00000515769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 2 publications found

Genes affected

LINC01091 (HGNC:27721): (long intergenic non-protein coding RNA 1091)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515769.1. 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
	LINC01091	NR_027105.3		n.629+25130C>T		intron	N/A
	LINC01091	NR_027106.2		n.206-9258C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01091	ENST00000515769.1	TSL:1	n.206-9258C>T		intron	N/A
	LINC01091	ENST00000508111.6	TSL:5	n.584+25130C>T		intron	N/A
	LINC01091	ENST00000511919.6	TSL:3	n.655+25130C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71508 AN: 151438 Hom.: 17353 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.472 AC: 71604 AN: 151556 Hom.: 17390 Cov.: 31 AF XY: 0.465 AC XY: 34394 AN XY: 74012

African (AFR) AF: 0.577 AC: 23825 AN: 41314

American (AMR) AF: 0.424 AC: 6460 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1691 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1794 AN: 5144

South Asian (SAS) AF: 0.364 AC: 1744 AN: 4786

European-Finnish (FIN) AF: 0.364 AC: 3818 AN: 10494

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30693 AN: 67832

Other (OTH) AF: 0.510 AC: 1071 AN: 2100

Alfa AF: 0.462 Hom.: 30995

Bravo AF: 0.487

Asia WGS AF: 0.417 AC: 1451 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs3113392; hg19: chr4-124775472;