ENST00000588794.1:n.347-9660A>G

Variant names:

• chr18-60151311-A-G
• rs74861148
• ENST00000588794.1:n.347-9660A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000588794.1(LINC03111):​n.347-9660A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00681 in 152,324 control chromosomes in the GnomAD database, including 37 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 0.0068 (37 hom., cov: 32)
• Consequence: LINC03111 ENST00000588794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 4 publications found

Genes affected

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

ENSG00000304301 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00681 (1037/152324) while in subpopulation AMR AF = 0.0489 (747/15278). AF 95% confidence interval is 0.046. There are 37 homozygotes in GnomAd4. There are 541 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 37 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03111	NR_186639.1	n.347-9660A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03111	ENST00000588794.1	n.347-9660A>G		intron_variant	Intron 2 of 2	3
ENSG00000304301	ENST00000801882.1	n.76-3729T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00683 AC: 1039 AN: 152206 Hom.: 38 Cov.: 32

Gnomad AFR AF: 0.00164

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0490

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000279

Gnomad OTH AF: 0.0100

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

GnomAD4 genome AF: 0.00681 AC: 1037 AN: 152324 Hom.: 37 Cov.: 32 AF XY: 0.00726 AC XY: 541 AN XY: 74484

African (AFR) AF: 0.00164 AC: 68 AN: 41578

American (AMR) AF: 0.0489 AC: 747 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.0336 AC: 174 AN: 5186

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000279 AC: 19 AN: 68038

Other (OTH) AF: 0.00947 AC: 20 AN: 2112

Alfa AF: 0.0230 Hom.: 54

Bravo AF: 0.0135

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.75
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs74861148; hg19: chr18-57818543;