chr1-112243075-T-C

Position:

• chr1-112243075-T-C

Variant summary

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

The NR_183466.1(LINC02884):​n.247-8176A>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 0.257 in 152,096 control chromosomes in the GnomAD database, including 5,352 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 0.26 (5352 hom., cov: 32)
• Consequence: LINC02884 NR_183466.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02884	NR_183466.1	n.247-8176A>G		intron_variant, non_coding_transcript_variant
LINC02884	NR_183465.1	n.247-4877A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02884	ENST00000427290.2	n.255-65462A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39085 AN: 151978 Hom.: 5346 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.257 AC: 39118 AN: 152096 Hom.: 5352 Cov.: 32 AF XY: 0.253 AC XY: 18816 AN XY: 74342

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.235

Alfa AF: 0.244 Hom.: 4645

Bravo AF: 0.258

Asia WGS AF: 0.136 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7551793; hg19: chr1-112785697;