rs11043097

Variant names:

• chr11-11114248-T-C
• rs11043097
• ENST00000647635.1:n.159-3588T>C

Variant summary

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

The ENST00000647635.1(LINC02752):​n.159-3588T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,194 control chromosomes in the GnomAD database, including 1,935 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 0.15 (1935 hom., cov: 32)
• Consequence: LINC02752 ENST00000647635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471
• Publications: 6 publications found

Genes affected

LINC02752 (HGNC:54272): (long intergenic non-protein coding RNA 2752)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.206 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
LINC02752	ENST00000647635.1	n.159-3588T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23313 AN: 152076 Hom.: 1933 Cov.: 32

Gnomad AFR AF: 0.0973

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.153 AC: 23316 AN: 152194 Hom.: 1935 Cov.: 32 AF XY: 0.154 AC XY: 11452 AN XY: 74398

African (AFR) AF: 0.0970 AC: 4031 AN: 41538

American (AMR) AF: 0.212 AC: 3235 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 664 AN: 3466

East Asian (EAS) AF: 0.190 AC: 982 AN: 5180

South Asian (SAS) AF: 0.172 AC: 829 AN: 4826

European-Finnish (FIN) AF: 0.120 AC: 1275 AN: 10598

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11772 AN: 68000

Other (OTH) AF: 0.161 AC: 341 AN: 2112

Alfa AF: 0.173 Hom.: 3932

Bravo AF: 0.155

Asia WGS AF: 0.152 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.5
DANN	Benign	0.65
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs11043097; hg19: chr11-11135795;