rs7117858

Positions:

• chr11-15672916-G-A
• chr11-15672916-G-C

Variant summary

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

The NR_169502.1(LINC02751):​n.756+28881G>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 0.752 in 152,018 control chromosomes in the GnomAD database, including 43,201 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 0.75 (43201 hom., cov: 32)
• Consequence: LINC02751 NR_169502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02751	NR_169502.1	n.756+28881G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000532242.2	n.365+28881G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114245 AN: 151900 Hom.: 43166 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.752 AC: 114333 AN: 152018 Hom.: 43201 Cov.: 32 AF XY: 0.749 AC XY: 55652 AN XY: 74304

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.755

Alfa AF: 0.777 Hom.: 54859

Bravo AF: 0.754

Asia WGS AF: 0.791 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.76
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7117858; hg19: chr11-15694462;