rs878953

chr5-164499486-G-A

Variant summary

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

The NR_105065.1(LOC102546299):n.258+12745G>A 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 0.474 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: LOC102546299 NR_105065.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

Genes affected

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

LOC102546299 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102546299	NR_105065.1	n.258+12745G>A		intron_variant, non_coding_transcript_variant
LINC03000	XR_001742489.2	n.576+145262G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03000	ENST00000519570.5	n.303+145262G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.455

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.46
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs878953; hg19: chr5-163926492;