rs11043097

Positions:

• chr11-11114248-T-C

Variant summary

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

The ENST00000647635.1(LINC02752):​n.159-3588T>C 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 0.153 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02752	ENST00000647635.1	n.159-3588T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0970

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.161

Alfa AF: 0.173 Hom.: 3119

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11043097; hg19: chr11-11135795;