3-109192185-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648541.1(LINC00488):n.903+8567C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,780 control chromosomes in the GnomAD database, including 33,666 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 0.66 (33666 hom., cov: 31)
• Consequence: LINC00488 ENST00000648541.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00488	ENST00000648541.1	n.903+8567C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100139 AN: 151662 Hom.: 33624 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.660 AC: 100232 AN: 151780 Hom.: 33666 Cov.: 31 AF XY: 0.656 AC XY: 48617 AN XY: 74120

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.647

Alfa AF: 0.671 Hom.: 4065

Bravo AF: 0.656

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.1
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163402; hg19: chr3-108911032;