rs2724432

Variant names:

• chr11-110413469-C-T
• rs2724432
• ENST00000796188.1:n.411-14269C>T

Variant summary

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

The ENST00000796188.1(LINC02732):​n.411-14269C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,246 control chromosomes in the GnomAD database, including 3,638 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 0.21 (3638 hom., cov: 33)
• Consequence: LINC02732 ENST00000796188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 4 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=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 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.411-14269C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 32011 AN: 152128 Hom.: 3635 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.210 AC: 32025 AN: 152246 Hom.: 3638 Cov.: 33 AF XY: 0.204 AC XY: 15180 AN XY: 74458

African (AFR) AF: 0.261 AC: 10849 AN: 41534

American (AMR) AF: 0.147 AC: 2249 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 751 AN: 3472

East Asian (EAS) AF: 0.0324 AC: 168 AN: 5186

South Asian (SAS) AF: 0.0829 AC: 400 AN: 4826

European-Finnish (FIN) AF: 0.217 AC: 2305 AN: 10602

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14708 AN: 68012

Other (OTH) AF: 0.197 AC: 416 AN: 2114

Alfa AF: 0.209 Hom.: 3173

Bravo AF: 0.209

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	6.6
DANN	Benign	0.88
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2724432; hg19: chr11-110284193;