18-60130586-A-G

Variant names:

• chr18-60130586-A-G
• rs17772748
• ENST00000588794.1:n.346+931A>G

Variant summary

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

The ENST00000588794.1(LINC03111):​n.346+931A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 152,238 control chromosomes in the GnomAD database, including 427 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 0.065 (427 hom., cov: 32)
• Consequence: LINC03111 ENST00000588794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 4 publications found

Genes affected

LINC03111 (HGNC:56850): (long intergenic non-protein coding RNA 3111)

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 (NFE) allele frequency at 95% confidence interval = 0.0912 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000588794.1. 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
	LINC03111	NR_186639.1		n.346+931A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03111	ENST00000588794.1	TSL:3	n.346+931A>G		intron	N/A
	LINC03111	ENST00000668793.1		n.240+931A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0652 AC: 9913 AN: 152120 Hom.: 428 Cov.: 32

Gnomad AFR AF: 0.0204

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0651 AC: 9908 AN: 152238 Hom.: 427 Cov.: 32 AF XY: 0.0622 AC XY: 4633 AN XY: 74436

African (AFR) AF: 0.0204 AC: 847 AN: 41568

American (AMR) AF: 0.0780 AC: 1191 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3468

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4830

European-Finnish (FIN) AF: 0.0556 AC: 589 AN: 10602

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0931 AC: 6329 AN: 67996

Other (OTH) AF: 0.0790 AC: 167 AN: 2114

Alfa AF: 0.0722 Hom.: 449

Bravo AF: 0.0669

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs17772748; hg19: chr18-57797818;