3-109199392-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.693

Alfa AF: 0.666 Hom.: 15756

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163397; hg19: chr3-108918239;