rs2564866

Positions:

• chr11-112276936-A-G

Variant summary

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

The NR_126004.1(LINC02762):​n.35+6153A>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 0.73 in 151,356 control chromosomes in the GnomAD database, including 40,374 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 0.73 (40374 hom., cov: 30)
• Consequence: LINC02762 NR_126004.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22

Genes affected

LINC02762 (HGNC:27443): (long intergenic non-protein coding RNA 2762)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02762	NR_126004.1	n.35+6153A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02762	ENST00000504610.2	n.35+6153A>G		intron_variant, non_coding_transcript_variant		2
LINC02762	ENST00000532168.3	n.37-3548A>G		intron_variant, non_coding_transcript_variant		3
LINC02762	ENST00000701675.1	n.37-3548A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110307 AN: 151238 Hom.: 40317 Cov.: 30

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.730 AC: 110426 AN: 151356 Hom.: 40374 Cov.: 30 AF XY: 0.729 AC XY: 53857 AN XY: 73910

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.737

Alfa AF: 0.724 Hom.: 4955

Bravo AF: 0.733

Asia WGS AF: 0.772 AC: 2685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.014
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: rs2564866; hg19: chr11-112147659;