11-15688538-T-G

Position:

• chr11-15688538-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_169502.1(LINC02751):​n.757-15795T>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 0.219 in 152,098 control chromosomes in the GnomAD database, including 3,845 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 0.22 (3845 hom., cov: 32)
• Consequence: LINC02751 NR_169502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02751	NR_169502.1	n.757-15795T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000532242.2	n.366-15795T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33222 AN: 151978 Hom.: 3839 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.219 AC: 33253 AN: 152098 Hom.: 3845 Cov.: 32 AF XY: 0.222 AC XY: 16505 AN XY: 74356

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.224

Alfa AF: 0.191 Hom.: 3473

Bravo AF: 0.217

Asia WGS AF: 0.181 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	14
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7108738; hg19: chr11-15710084;