rs3113384

Variant names:

• chr4-123777822-A-G
• rs3113384
• ENST00000515769.1:n.112+3447A>G

Variant summary

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

The ENST00000515769.1(LINC01091):​n.112+3447A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,144 control chromosomes in the GnomAD database, including 1,279 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 0.13 (1279 hom., cov: 32)
• Consequence: LINC01091 ENST00000515769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 1 publications found

Genes affected

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

ENSG00000304279 (HGNC:):

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 = 0.147 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01091	NR_027105.3		n.537-51273A>G		intron	N/A
	LINC01091	NR_027106.2		n.112+3447A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01091	ENST00000515769.1	TSL:1	n.112+3447A>G		intron	N/A
	LINC01091	ENST00000508111.6	TSL:5	n.492-51273A>G		intron	N/A
	LINC01091	ENST00000511919.6	TSL:3	n.563-51273A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19338 AN: 152026 Hom.: 1278 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.127 AC: 19365 AN: 152144 Hom.: 1279 Cov.: 32 AF XY: 0.130 AC XY: 9663 AN XY: 74384

African (AFR) AF: 0.140 AC: 5820 AN: 41516

American (AMR) AF: 0.0974 AC: 1488 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3470

East Asian (EAS) AF: 0.156 AC: 809 AN: 5182

South Asian (SAS) AF: 0.152 AC: 731 AN: 4822

European-Finnish (FIN) AF: 0.156 AC: 1651 AN: 10574

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8264 AN: 67980

Other (OTH) AF: 0.114 AC: 241 AN: 2116

Alfa AF: 0.123 Hom.: 129

Bravo AF: 0.123

Asia WGS AF: 0.187 AC: 649 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.23
DANN	Benign	0.61
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs3113384; hg19: chr4-124698977;