chr11-15679072-T-A

Position:

• chr11-15679072-T-A

Variant summary

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

The NR_169502.1(LINC02751):​n.757-25261T>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 0.286 in 151,484 control chromosomes in the GnomAD database, including 6,436 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 0.29 (6436 hom., cov: 33)
• Consequence: LINC02751 NR_169502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02751	NR_169502.1	n.757-25261T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000532242.2	n.366-25261T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43304 AN: 151364 Hom.: 6403 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.286 AC: 43389 AN: 151484 Hom.: 6436 Cov.: 33 AF XY: 0.293 AC XY: 21702 AN XY: 74056

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.282

Alfa AF: 0.270 Hom.: 708

Bravo AF: 0.290

Asia WGS AF: 0.352 AC: 1220 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2351061; hg19: chr11-15700618;