rs7551793

Variant names:

• chr1-112243075-T-C
• rs7551793
• ENST00000427290.2:n.255-65462A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000427290.2(LINC02884):​n.255-65462A>G variant causes a intron 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 ENST00000427290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 1 publications found

Genes affected

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

ENSG00000297559 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427290.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02884	NR_183465.1		n.247-4877A>G		intron	N/A
	LINC02884	NR_183466.1		n.247-8176A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02884	ENST00000427290.2	TSL:3	n.255-65462A>G		intron	N/A
	LINC02884	ENST00000654472.1		n.400-8176A>G		intron	N/A
	LINC02884	ENST00000658120.2		n.353-8176A>G		intron	N/A

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

African (AFR) AF: 0.347 AC: 14396 AN: 41452

American (AMR) AF: 0.182 AC: 2783 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3470

East Asian (EAS) AF: 0.138 AC: 710 AN: 5156

South Asian (SAS) AF: 0.152 AC: 733 AN: 4826

European-Finnish (FIN) AF: 0.223 AC: 2356 AN: 10588

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16595 AN: 67998

Other (OTH) AF: 0.235 AC: 496 AN: 2110

Alfa AF: 0.246 Hom.: 6169

Bravo AF: 0.258

Asia WGS AF: 0.136 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.74
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs7551793; hg19: chr1-112785697;