8-48624087-T-C

Variant names:

• chr8-48624087-T-C
• rs2279301
• ENST00000522575.1:n.357-71337T>C

Variant summary

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

The ENST00000522575.1(ENSG00000253608):​n.357-71337T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,946 control chromosomes in the GnomAD database, including 9,857 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 0.34 (9857 hom., cov: 32)
• Consequence: ENSG00000253608 ENST00000522575.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 5 publications found

Genes affected

ENSG00000253608 (HGNC:):

LINC03054 (HGNC:56349): (long intergenic non-protein coding RNA 3054)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522575.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101929268	NR_105002.1		n.357-71337T>C		intron	N/A
	LINC03054	NR_105004.1		n.*192T>C		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253608	ENST00000522575.1	TSL:2	n.357-71337T>C		intron	N/A
	LINC03054	ENST00000521660.2	TSL:3	n.*180T>C		downstream_gene	N/A
	LINC03054	ENST00000795396.1		n.*196T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52097 AN: 151828 Hom.: 9827 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.343 AC: 52167 AN: 151946 Hom.: 9857 Cov.: 32 AF XY: 0.343 AC XY: 25500 AN XY: 74290

African (AFR) AF: 0.499 AC: 20654 AN: 41380

American (AMR) AF: 0.316 AC: 4823 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1544 AN: 5152

South Asian (SAS) AF: 0.471 AC: 2269 AN: 4816

European-Finnish (FIN) AF: 0.216 AC: 2287 AN: 10596

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.265 AC: 17994 AN: 67964

Other (OTH) AF: 0.354 AC: 745 AN: 2102

Alfa AF: 0.298 Hom.: 3741

Bravo AF: 0.353

Asia WGS AF: 0.430 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.30
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2279301; hg19: chr8-49536647;