rs1604797

chr11-11111902-T-A

Variant summary

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

The ENST00000647635.1(LINC02752):n.159-5934T>A 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 0.276 in 151,946 control chromosomes in the GnomAD database, including 5,996 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 0.28 (5996 hom., cov: 32)
• Consequence: LINC02752 ENST00000647635.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02752	ENST00000647635.1	n.159-5934T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41909 AN: 151828 Hom.: 5976 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.276 AC: 41975 AN: 151946 Hom.: 5996 Cov.: 32 AF XY: 0.271 AC XY: 20156 AN XY: 74304

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.269

Alfa AF: 0.273 Hom.: 705

Bravo AF: 0.285

Asia WGS AF: 0.175 AC: 610 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.41
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1604797; hg19: chr11-11133449;