rs11102457

Positions:

• chr1-112323975-G-A

Variant summary

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

The NR_183466.1(LINC02884):​n.246+36387C>T 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 0.155 in 152,200 control chromosomes in the GnomAD database, including 1,858 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 0.15 (1858 hom., cov: 33)
• Consequence: LINC02884 NR_183466.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403

Genes affected

LINC02884 (HGNC:54808): (long intergenic non-protein coding RNA 2884)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02884	NR_183466.1	n.246+36387C>T		intron_variant, non_coding_transcript_variant
LINC02884	NR_183465.1	n.246+36387C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02884	ENST00000427290.2	n.254+36387C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23568 AN: 152082 Hom.: 1858 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.155 AC: 23582 AN: 152200 Hom.: 1858 Cov.: 33 AF XY: 0.155 AC XY: 11557 AN XY: 74414

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.133

Alfa AF: 0.149 Hom.: 2416

Bravo AF: 0.148

Asia WGS AF: 0.204 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11102457; hg19: chr1-112866597;