11-128175071-A-G

Position:

• chr11-128175071-A-G

Variant summary

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

The NR_183639.1(LINC02725):​n.703-5389A>G 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 0.24 in 152,108 control chromosomes in the GnomAD database, including 4,895 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 0.24 (4895 hom., cov: 33)
• Consequence: LINC02725 NR_183639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

LINC02725 (HGNC:54242): (long intergenic non-protein coding RNA 2725)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02725	NR_183639.1	n.703-5389A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02725	ENST00000664091.1	n.485-5389A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36537 AN: 151990 Hom.: 4886 Cov.: 33

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.240 AC: 36574 AN: 152108 Hom.: 4895 Cov.: 33 AF XY: 0.240 AC XY: 17870 AN XY: 74372

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.273

Alfa AF: 0.180 Hom.: 5499

Bravo AF: 0.255

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7948482; hg19: chr11-128044966;