3-109199392-C-T

Variant names:

• chr3-109199392-C-T
• rs1163397
• ENST00000648541.1:n.903+15774C>T

Variant summary

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

The ENST00000648541.1(LINC00488):​n.903+15774C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,070 control chromosomes in the GnomAD database, including 38,572 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 0.70 (38572 hom., cov: 32)
• Consequence: LINC00488 ENST00000648541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 4 publications found

Genes affected

LINC00488 (HGNC:32675): (long intergenic non-protein coding RNA 488)

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 (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00488	ENST00000648541.1	n.903+15774C>T		intron_variant	Intron 3 of 3
LINC00488	ENST00000743424.1	n.348-16503C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106833 AN: 151952 Hom.: 38523 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.703 AC: 106933 AN: 152070 Hom.: 38572 Cov.: 32 AF XY: 0.697 AC XY: 51812 AN XY: 74344

African (AFR) AF: 0.830 AC: 34429 AN: 41496

American (AMR) AF: 0.638 AC: 9746 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2288 AN: 3472

East Asian (EAS) AF: 0.293 AC: 1515 AN: 5162

South Asian (SAS) AF: 0.563 AC: 2713 AN: 4822

European-Finnish (FIN) AF: 0.694 AC: 7329 AN: 10554

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46613 AN: 67960

Other (OTH) AF: 0.693 AC: 1463 AN: 2112

Alfa AF: 0.670 Hom.: 17861

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.36
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1163397; hg19: chr3-108918239;