rs878953

Variant names:

• chr5-164499486-G-A
• rs878953
• ENST00000486913.3:n.158+12745G>A

Variant summary

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

The ENST00000486913.3(LINC03000):​n.158+12745G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,910 control chromosomes in the GnomAD database, including 18,293 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 0.47 (18293 hom., cov: 32)
• Consequence: LINC03000 ENST00000486913.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 6 publications found

Genes affected

LINC03000 (HGNC:56116): (long intergenic non-protein coding RNA 3000)

LOC102546299 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000486913.3. 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
	LOC102546299	NR_105065.1		n.258+12745G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03000	ENST00000486913.3	TSL:2	n.158+12745G>A		intron	N/A
	LINC03000	ENST00000517508.5	TSL:4	n.658+12745G>A		intron	N/A
	LINC03000	ENST00000519327.5	TSL:3	n.458+12745G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71874 AN: 151790 Hom.: 18257 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.474 AC: 71972 AN: 151910 Hom.: 18293 Cov.: 32 AF XY: 0.470 AC XY: 34932 AN XY: 74250

African (AFR) AF: 0.657 AC: 27214 AN: 41412

American (AMR) AF: 0.470 AC: 7170 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1545 AN: 3468

East Asian (EAS) AF: 0.190 AC: 981 AN: 5164

South Asian (SAS) AF: 0.348 AC: 1679 AN: 4818

European-Finnish (FIN) AF: 0.409 AC: 4321 AN: 10554

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27568 AN: 67926

Other (OTH) AF: 0.455 AC: 957 AN: 2102

Alfa AF: 0.457 Hom.: 2031

Bravo AF: 0.488

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.41
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs878953; hg19: chr5-163926492;