3-109192185-C-T

Variant names:

• chr3-109192185-C-T
• rs1163402
• ENST00000648541.1:n.903+8567C>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+8567C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 1 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=-0.95).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00488	ENST00000648541.1	n.903+8567C>T		intron_variant	Intron 3 of 3
LINC00488	ENST00000743424.1	n.347+13617C>T		intron_variant	Intron 2 of 2
LINC00488	ENST00000743425.1	n.327-5509C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.730 AC: 30238 AN: 41400

American (AMR) AF: 0.611 AC: 9318 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2119 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1436 AN: 5110

South Asian (SAS) AF: 0.552 AC: 2646 AN: 4796

European-Finnish (FIN) AF: 0.684 AC: 7181 AN: 10504

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45113 AN: 67936

Other (OTH) AF: 0.647 AC: 1367 AN: 2112

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
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs1163402; hg19: chr3-108911032;