rs4754450

Variant names:

• chr11-110426324-T-C
• rs4754450
• ENST00000796188.1:n.411-1414T>C

Variant summary

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

The ENST00000796188.1(LINC02732):​n.411-1414T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,012 control chromosomes in the GnomAD database, including 21,930 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 0.52 (21930 hom., cov: 32)
• Consequence: LINC02732 ENST00000796188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 11 publications found

Genes affected

LINC02732 (HGNC:54249): (long intergenic non-protein coding RNA 2732)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 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
LINC02732	ENST00000796188.1	n.411-1414T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78714 AN: 151894 Hom.: 21878 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.519 AC: 78829 AN: 152012 Hom.: 21930 Cov.: 32 AF XY: 0.520 AC XY: 38664 AN XY: 74294

African (AFR) AF: 0.717 AC: 29733 AN: 41440

American (AMR) AF: 0.557 AC: 8505 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1489 AN: 3468

East Asian (EAS) AF: 0.634 AC: 3279 AN: 5172

South Asian (SAS) AF: 0.448 AC: 2154 AN: 4806

European-Finnish (FIN) AF: 0.447 AC: 4712 AN: 10548

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27478 AN: 67982

Other (OTH) AF: 0.497 AC: 1048 AN: 2110

Alfa AF: 0.525 Hom.: 5482

Bravo AF: 0.539

Asia WGS AF: 0.566 AC: 1968 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	3.0
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4754450; hg19: chr11-110297048;